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Biotechnology Information sequence contigs data
Reads per exon kilobase per million (RPKM) values-based expression analysis of uridine diphosphate glycosyltransferases ( UGTs ) in P. kurrooa transcriptome . Expression of 17 UGTs was studied at 15°C and 25°C. Details of the corresponding <t>contigs,</t> accession number and BLAST are listed in Additional file 15 .
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Images

1) Product Images from "De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments"

Article Title: De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments

Journal: BMC Genomics

doi: 10.1186/1471-2164-13-126

Reads per exon kilobase per million (RPKM) values-based expression analysis of uridine diphosphate glycosyltransferases ( UGTs ) in P. kurrooa transcriptome . Expression of 17 UGTs was studied at 15°C and 25°C. Details of the corresponding contigs, accession number and BLAST are listed in Additional file 15 .
Figure Legend Snippet: Reads per exon kilobase per million (RPKM) values-based expression analysis of uridine diphosphate glycosyltransferases ( UGTs ) in P. kurrooa transcriptome . Expression of 17 UGTs was studied at 15°C and 25°C. Details of the corresponding contigs, accession number and BLAST are listed in Additional file 15 .

Techniques Used: Expressing

2) Product Images from "Insights into the transcriptional and translational mechanisms of linear organellar chromosomes in the box jellyfish Alatina alata (Cnidaria: Medusozoa: Cubozoa)"

Article Title: Insights into the transcriptional and translational mechanisms of linear organellar chromosomes in the box jellyfish Alatina alata (Cnidaria: Medusozoa: Cubozoa)

Journal: RNA Biology

doi: 10.1080/15476286.2016.1194161

Secondary structure of the putative origin of translation (OT) found on all 8 chromosomes of the mt genome of Alatina alata using the DNA folding program from the mfold Web Server with default parameters. The greyed area is present at the DNA level but
Figure Legend Snippet: Secondary structure of the putative origin of translation (OT) found on all 8 chromosomes of the mt genome of Alatina alata using the DNA folding program from the mfold Web Server with default parameters. The greyed area is present at the DNA level but

Techniques Used:

Mitochondrial read coverage values in the mtDNA of Alatina alata . (A) Nucleotide coverage of the unique regions of individual mitochondrial genes from the DNA-seq and RNA-seq data. (B) Nucleotide coverage of the unique regions of mitochondrial chromosomes
Figure Legend Snippet: Mitochondrial read coverage values in the mtDNA of Alatina alata . (A) Nucleotide coverage of the unique regions of individual mitochondrial genes from the DNA-seq and RNA-seq data. (B) Nucleotide coverage of the unique regions of mitochondrial chromosomes

Techniques Used: DNA Sequencing, RNA Sequencing Assay

Expression of mt genes in Alatina alata
Figure Legend Snippet: Expression of mt genes in Alatina alata

Techniques Used: Expressing

Gene expression in the mitochondrion of Alatina alata . (A) Pattern of gene expression and their coverage in the DNA-seq and RNA-seq data sets for a model mito-chromosome. Graphs of read coverage do not correspond to the true values, but rather approximate
Figure Legend Snippet: Gene expression in the mitochondrion of Alatina alata . (A) Pattern of gene expression and their coverage in the DNA-seq and RNA-seq data sets for a model mito-chromosome. Graphs of read coverage do not correspond to the true values, but rather approximate

Techniques Used: Expressing, DNA Sequencing, RNA Sequencing Assay

Expression of mt genes in Alatina alata
Figure Legend Snippet: Expression of mt genes in Alatina alata

Techniques Used: Expressing

3) Product Images from "Variation among S-locus haplotypes and among stylar RNases in almond"

Article Title: Variation among S-locus haplotypes and among stylar RNases in almond

Journal: Scientific Reports

doi: 10.1038/s41598-020-57498-6

S -locus structure. Structure of the almond S locus showing the positions of the SLF , S-RNase and SFB genes and long terminal repeat retrotransposons (LTRs). Black lines indicate regions for which sequences were obtained and grey lines indicate gaps in the sequence.
Figure Legend Snippet: S -locus structure. Structure of the almond S locus showing the positions of the SLF , S-RNase and SFB genes and long terminal repeat retrotransposons (LTRs). Black lines indicate regions for which sequences were obtained and grey lines indicate gaps in the sequence.

Techniques Used: Sequencing

4) Product Images from "Insights into the biogenesis and potential functions of exonic circular RNA"

Article Title: Insights into the biogenesis and potential functions of exonic circular RNA

Journal: Scientific Reports

doi: 10.1038/s41598-018-37037-0

Exonic features at human HEK 293 cell circRNA-producing gene loci. ( a ) Relative frequencies of exons by ordinal position N along circRNA-producing genes. Frequency of back-splice ( b ) acceptor and ( c ) donor exon at each position after normalisation to exon frequency as shown in ( a ). *CircRNA acceptor exons were over-represented in the second position of circRNA-producing genes compared to other exon positions (P-value
Figure Legend Snippet: Exonic features at human HEK 293 cell circRNA-producing gene loci. ( a ) Relative frequencies of exons by ordinal position N along circRNA-producing genes. Frequency of back-splice ( b ) acceptor and ( c ) donor exon at each position after normalisation to exon frequency as shown in ( a ). *CircRNA acceptor exons were over-represented in the second position of circRNA-producing genes compared to other exon positions (P-value

Techniques Used: Significance Assay

Selection of human translation candidate (tc-) circRNAs from Transcript Isoform in Polysomes sequencing (TrIP-seq) data. ( a ) UV absorbance profile after separating cycloheximide-treated cytoplasmic HEK 293 cell extract, showing how RNA co-sedimenting with different (poly)ribosomal fractions was collected and sequenced separately. Figure reproduced with modifications, and non-processed sequencing data taken, from the original publication 50 . ( b ) Relative abundance of circRNA (JPM; green) and cognate linear mRNA (RPM; striped) overall for the entire set of HEK circRNAs (left) and across (poly)ribosome co-sedimenting and non-associated (free*; calculated) RNA (right). ( c ) Same as ( b ), but comparing the presence of circRNAs (counts of unique back-spliced junctions) to that of the corresponding cognate linear mRNAs. *’Free’ denotes RNA pool not associated with ribosomes calculated from counts in ribosomal fractions and total cellular RNA as indicated in panel (a) (also see ‘Detection of circRNAs in ribosome sedimentation profiles’ subsection in the Methods for details).
Figure Legend Snippet: Selection of human translation candidate (tc-) circRNAs from Transcript Isoform in Polysomes sequencing (TrIP-seq) data. ( a ) UV absorbance profile after separating cycloheximide-treated cytoplasmic HEK 293 cell extract, showing how RNA co-sedimenting with different (poly)ribosomal fractions was collected and sequenced separately. Figure reproduced with modifications, and non-processed sequencing data taken, from the original publication 50 . ( b ) Relative abundance of circRNA (JPM; green) and cognate linear mRNA (RPM; striped) overall for the entire set of HEK circRNAs (left) and across (poly)ribosome co-sedimenting and non-associated (free*; calculated) RNA (right). ( c ) Same as ( b ), but comparing the presence of circRNAs (counts of unique back-spliced junctions) to that of the corresponding cognate linear mRNAs. *’Free’ denotes RNA pool not associated with ribosomes calculated from counts in ribosomal fractions and total cellular RNA as indicated in panel (a) (also see ‘Detection of circRNAs in ribosome sedimentation profiles’ subsection in the Methods for details).

Techniques Used: Selection, Sequencing, Sedimentation

NET-seq signal values (reflecting inverse Pol II speed across mRNA-coding genes) compared between circRNAs of HEK 293 (green; a , b ) or HeLa (grey; c , d ) cells 52 and the corresponding position-adjusted exons and introns (dark green, white; see ‘Custom reference datasets’ in Methods). ( a , c ) Comparisons among the upstream intron, circRNA exon and downstream intron of single-exon circRNAs (left to right; corresponds to the schematic on top). ( b , d ) Comparisons among the acceptor intron, acceptor exon, internal intron, internal exon, donor exon and donor intron of multi-exon circRNAs (left to right; corresponds to the schematic on top). Asterisks denote significantly different NET-seq signal between the circRNAs and corresponding exon and intron regions in the reference (P-values
Figure Legend Snippet: NET-seq signal values (reflecting inverse Pol II speed across mRNA-coding genes) compared between circRNAs of HEK 293 (green; a , b ) or HeLa (grey; c , d ) cells 52 and the corresponding position-adjusted exons and introns (dark green, white; see ‘Custom reference datasets’ in Methods). ( a , c ) Comparisons among the upstream intron, circRNA exon and downstream intron of single-exon circRNAs (left to right; corresponds to the schematic on top). ( b , d ) Comparisons among the acceptor intron, acceptor exon, internal intron, internal exon, donor exon and donor intron of multi-exon circRNAs (left to right; corresponds to the schematic on top). Asterisks denote significantly different NET-seq signal between the circRNAs and corresponding exon and intron regions in the reference (P-values

Techniques Used:

Patterns of NET-seq signal values (reflecting inverse Pol II speed across mRNA-coding genes) compared between circRNAs and the corresponding position-adjusted exons and introns (see ‘Custom reference datasets’ in Methods) in HEK 293 ( a – c ) and HeLa ( d – f ) cells 52 . NET-seq signals were averaged for different regions of circRNA-producing genes (( a – c ), green line; ( d – f ), grey line) and the corresponding position- and expression-adjusted RefSeq average (( a – c ), green line; ( d – f ), grey line), as depicted in the schematic on top. NET-seq signal values around acceptor are shown with exon 2 acceptors ( a , d ) and with exon 3 or higher acceptors ( b , e ). ( c , f ) Shows NET-seq signal values around internal circRNA exons and donor exons. To better resolve signals, different discontinuous scaling is used on the X-axis. Coverage of the intronic sequences is represented as an average in each position for a 300 nt region, beginning at the adjacent exon (natural scale). Exonic coverage was first scaled to units of exon length and then averaged (justified scale). Regions focussed on the next upstream or downstream exons are also shown. Signal for regions focussed on circRNA-internal exons were averaged across all instances of their type. Boxplots on the top of the chart represent average NET-seq signal (Pol II occupancy) over the respective regions and have the same scale for each cell type and are aligned by zero for all regions except first introns and exons (position- and expression-adjusted RefSeq values for HeLa are shown as white boxes). Asterisks denote significantly different NET-seq signal between the circRNAs and corresponding regions in the reference (P-values
Figure Legend Snippet: Patterns of NET-seq signal values (reflecting inverse Pol II speed across mRNA-coding genes) compared between circRNAs and the corresponding position-adjusted exons and introns (see ‘Custom reference datasets’ in Methods) in HEK 293 ( a – c ) and HeLa ( d – f ) cells 52 . NET-seq signals were averaged for different regions of circRNA-producing genes (( a – c ), green line; ( d – f ), grey line) and the corresponding position- and expression-adjusted RefSeq average (( a – c ), green line; ( d – f ), grey line), as depicted in the schematic on top. NET-seq signal values around acceptor are shown with exon 2 acceptors ( a , d ) and with exon 3 or higher acceptors ( b , e ). ( c , f ) Shows NET-seq signal values around internal circRNA exons and donor exons. To better resolve signals, different discontinuous scaling is used on the X-axis. Coverage of the intronic sequences is represented as an average in each position for a 300 nt region, beginning at the adjacent exon (natural scale). Exonic coverage was first scaled to units of exon length and then averaged (justified scale). Regions focussed on the next upstream or downstream exons are also shown. Signal for regions focussed on circRNA-internal exons were averaged across all instances of their type. Boxplots on the top of the chart represent average NET-seq signal (Pol II occupancy) over the respective regions and have the same scale for each cell type and are aligned by zero for all regions except first introns and exons (position- and expression-adjusted RefSeq values for HeLa are shown as white boxes). Asterisks denote significantly different NET-seq signal between the circRNAs and corresponding regions in the reference (P-values

Techniques Used: Expressing

Linear isoform diversity of human HEK 293 cell circRNA-producing genes. ( a ) mRNA isoform frequency of circRNA-producing genes (green) compared to all human RefSeq genes (dark green). ( b ) Same as ( a ), but compared to exon-count-adjusted genes (dark green). ( c ) Same as ( b ), but compared to gene-length-adjusted genes (dark green). ( d ) Exon counts in circRNA-producing genes compared to RefSeq genes. ( e ) Same as ( d ) but for gene lengths (binned in 20,000 bp steps). ( f – h ) As ( a – c ) but circRNAs are counted as additional transcript isoforms for each gene. Designations and abbreviations as in Fig. 1 . The distributions of data in ( a , d – f and h ) are significantly different between circRNA-producing and reference genes (P-value
Figure Legend Snippet: Linear isoform diversity of human HEK 293 cell circRNA-producing genes. ( a ) mRNA isoform frequency of circRNA-producing genes (green) compared to all human RefSeq genes (dark green). ( b ) Same as ( a ), but compared to exon-count-adjusted genes (dark green). ( c ) Same as ( b ), but compared to gene-length-adjusted genes (dark green). ( d ) Exon counts in circRNA-producing genes compared to RefSeq genes. ( e ) Same as ( d ) but for gene lengths (binned in 20,000 bp steps). ( f – h ) As ( a – c ) but circRNAs are counted as additional transcript isoforms for each gene. Designations and abbreviations as in Fig. 1 . The distributions of data in ( a , d – f and h ) are significantly different between circRNA-producing and reference genes (P-value

Techniques Used: Significance Assay

Exon lengths at human HEK 293 cell circRNA loci. Exons from circRNA-producing genes (green) are compared to RefSeq ( a – c ) or HEK-specific RefSeq ( d , e ) averages in the corresponding linear ordinal positions (dark green). ( a ) Average acceptor exon lengths. ( b ) Same as ( a ), but for donor exons. ( c ) Same as ( a ), but for circRNA-internal exons. ( d ) Single-exon circRNAs (green) compared to the internal exon lengths of HEK-specific RefSeq mRNAs (dark green). ( e ) Same as ( d ), but for acceptor (X1), donor (X2) and internal (X3) exons of multi-exon circRNAs. ( d , e ) Asterisks denote significantly different exon lengths between the circRNA-producing genes and HEK-specific RefSeq mRNAs (P-values
Figure Legend Snippet: Exon lengths at human HEK 293 cell circRNA loci. Exons from circRNA-producing genes (green) are compared to RefSeq ( a – c ) or HEK-specific RefSeq ( d , e ) averages in the corresponding linear ordinal positions (dark green). ( a ) Average acceptor exon lengths. ( b ) Same as ( a ), but for donor exons. ( c ) Same as ( a ), but for circRNA-internal exons. ( d ) Single-exon circRNAs (green) compared to the internal exon lengths of HEK-specific RefSeq mRNAs (dark green). ( e ) Same as ( d ), but for acceptor (X1), donor (X2) and internal (X3) exons of multi-exon circRNAs. ( d , e ) Asterisks denote significantly different exon lengths between the circRNA-producing genes and HEK-specific RefSeq mRNAs (P-values

Techniques Used:

Detection of human and mouse circRNAs in paired-end RNA-seq data 50 , 51 . ( a ) Schematic of the computational pipeline that discards (red ) read pairs that map to the linear transcriptome and identifies pairs where one read maps to a back-spliced junction while the other read maps within the exon span of the putative circRNA (green ). Denotes canonical linear-spliced junction, denotes back-spliced junction. Numbers indicate ‘linear’ ordinal exon position in a gene. ( b ) Numbers of predicted circRNAs (‘junctions’) with ≥0.1 junction per million of reads (JPM), circRNA-producing loci (‘genes’), and related RefSeq mRNA isoforms in MEF cells (blue), mouse heart (MH; red) and HEK 293 cells (green). ( c ) Overlap of circRNA-producing genes between all three sources. ( d ) Overlap of circRNAs identified in the different mouse sources.
Figure Legend Snippet: Detection of human and mouse circRNAs in paired-end RNA-seq data 50 , 51 . ( a ) Schematic of the computational pipeline that discards (red ) read pairs that map to the linear transcriptome and identifies pairs where one read maps to a back-spliced junction while the other read maps within the exon span of the putative circRNA (green ). Denotes canonical linear-spliced junction, denotes back-spliced junction. Numbers indicate ‘linear’ ordinal exon position in a gene. ( b ) Numbers of predicted circRNAs (‘junctions’) with ≥0.1 junction per million of reads (JPM), circRNA-producing loci (‘genes’), and related RefSeq mRNA isoforms in MEF cells (blue), mouse heart (MH; red) and HEK 293 cells (green). ( c ) Overlap of circRNA-producing genes between all three sources. ( d ) Overlap of circRNAs identified in the different mouse sources.

Techniques Used: RNA Sequencing Assay

Intron lengths at human HEK 293 cell circRNA loci. Introns from circRNA-producing genes (green) are compared to RefSeq averages in the corresponding linear ordinal positions (dark green). ( a ) Average intron lengths at the upstream flank of back-spliced acceptor exons. ( b ) Same as ( a ), but for introns at the downstream flank of back-spliced donor exons. ( a , b ) Acceptor and donor introns of circRNA-producing genes are much longer than RefSeq genes in same ordinal positions and overall lengths of acceptor and donor introns were significantly longer than introns of RefSeq genes (measured by P-value
Figure Legend Snippet: Intron lengths at human HEK 293 cell circRNA loci. Introns from circRNA-producing genes (green) are compared to RefSeq averages in the corresponding linear ordinal positions (dark green). ( a ) Average intron lengths at the upstream flank of back-spliced acceptor exons. ( b ) Same as ( a ), but for introns at the downstream flank of back-spliced donor exons. ( a , b ) Acceptor and donor introns of circRNA-producing genes are much longer than RefSeq genes in same ordinal positions and overall lengths of acceptor and donor introns were significantly longer than introns of RefSeq genes (measured by P-value

Techniques Used:

5) Product Images from "Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics"

Article Title: Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics

Journal: Environmental Microbiology

doi: 10.1111/1462-2920.12301

Heatmap of COGs showing only those that were either significantly over- (A) and under-represented (B) in freshwater metagenomes when compared with marine metagenomes after resampling and normalization against single-copy core COGs. Significantly over- and under-represented COGs were identified by Wilcoxon test ( P
Figure Legend Snippet: Heatmap of COGs showing only those that were either significantly over- (A) and under-represented (B) in freshwater metagenomes when compared with marine metagenomes after resampling and normalization against single-copy core COGs. Significantly over- and under-represented COGs were identified by Wilcoxon test ( P

Techniques Used:

Non-metric multidimensional scaling plot of microbial functional diversity along a productivity gradient (stress-value = 0.10). This plot is based on Horn–Morisita distances from COGs lists of 12 freshwater metagenomes. Total phosphors (TP) was mapped as en environmental variable vector onto the ordination using R function (TP) ‘envfit’. NMDS, Non-parametric-Multi-Dimensional-Scaling.
Figure Legend Snippet: Non-metric multidimensional scaling plot of microbial functional diversity along a productivity gradient (stress-value = 0.10). This plot is based on Horn–Morisita distances from COGs lists of 12 freshwater metagenomes. Total phosphors (TP) was mapped as en environmental variable vector onto the ordination using R function (TP) ‘envfit’. NMDS, Non-parametric-Multi-Dimensional-Scaling.

Techniques Used: Functional Assay, Plasmid Preparation

6) Product Images from "Threatened Corals Provide Underexplored Microbial Habitats"

Article Title: Threatened Corals Provide Underexplored Microbial Habitats

Journal: PLoS ONE

doi: 10.1371/journal.pone.0009554

V6-tag abundance profiles, similarity clustering, and taxonomic composition of bacterial communities. (A) Rank abundance curve for V6-tags detected in reef water superimposed with abundances found in coral samples shown as vertical colored bars. (B) Abundances of V6-tags, which were detected exclusively in corals, are shown alphabetically sorted by taxonomic classification of V6-tags (x-axis). In (A) and (B), circles denote log-scaled abundances of nearly full-length 16S rRNA gene sequences that were mapped to the respective V6-tag sequences. (C) Taxonomic composition of all samples and dendrogram of OTU abundances showing similarities between samples, which are color-coded according coral host taxonomy. Details on the taxonomic composition of each sample can be found in Table S1 . Abbreviations used: Acer = Acropora cervicornis ; Apal = Acropora palmata ; Dstr = Diploria strigosa ; Gven = Gorgonia ventalina ; Mfav = Montastraea faveolata ; Mfra = Montastraea franksi ; Past = Porites astreoides ; Reef = reef water.
Figure Legend Snippet: V6-tag abundance profiles, similarity clustering, and taxonomic composition of bacterial communities. (A) Rank abundance curve for V6-tags detected in reef water superimposed with abundances found in coral samples shown as vertical colored bars. (B) Abundances of V6-tags, which were detected exclusively in corals, are shown alphabetically sorted by taxonomic classification of V6-tags (x-axis). In (A) and (B), circles denote log-scaled abundances of nearly full-length 16S rRNA gene sequences that were mapped to the respective V6-tag sequences. (C) Taxonomic composition of all samples and dendrogram of OTU abundances showing similarities between samples, which are color-coded according coral host taxonomy. Details on the taxonomic composition of each sample can be found in Table S1 . Abbreviations used: Acer = Acropora cervicornis ; Apal = Acropora palmata ; Dstr = Diploria strigosa ; Gven = Gorgonia ventalina ; Mfav = Montastraea faveolata ; Mfra = Montastraea franksi ; Past = Porites astreoides ; Reef = reef water.

Techniques Used:

7) Product Images from "Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species"

Article Title: Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species

Journal: Genetics

doi: 10.1534/genetics.115.183152

Estimates of purifying and positive selection at 0-fold nonsynonymous sites in three Populus species. (A) The distribution of fitness effects of new amino acid mutations, (B) the proportion of adaptive substitution (α), and (C) the rate of adaptive nonsynonymous-to-synonymous substitutions (ω) in P. tremula (orange bar), P. tremuloides (blue bar), and P. trichocarpa (green bar). Error bars represent 95% bootstrap confidence intervals.
Figure Legend Snippet: Estimates of purifying and positive selection at 0-fold nonsynonymous sites in three Populus species. (A) The distribution of fitness effects of new amino acid mutations, (B) the proportion of adaptive substitution (α), and (C) the rate of adaptive nonsynonymous-to-synonymous substitutions (ω) in P. tremula (orange bar), P. tremuloides (blue bar), and P. trichocarpa (green bar). Error bars represent 95% bootstrap confidence intervals.

Techniques Used: Selection

Correlations of estimates between neutral genetic diversity (Θ fourfold ) (left), neutral genetic divergence ( d fourfold ) (right), and population-scaled recombination rates ( ρ ) over 1-Mb nonoverlapping windows. Linear regression lines are colored according to species: (A) P. tremula (orange line), (B) P. tremuloides (blue line), and (C) P. trichocarpa (green line).
Figure Legend Snippet: Correlations of estimates between neutral genetic diversity (Θ fourfold ) (left), neutral genetic divergence ( d fourfold ) (right), and population-scaled recombination rates ( ρ ) over 1-Mb nonoverlapping windows. Linear regression lines are colored according to species: (A) P. tremula (orange line), (B) P. tremuloides (blue line), and (C) P. trichocarpa (green line).

Techniques Used:

Correlations of estimates between (A) population-scaled recombination rates ( ρ ), (B) genic genetic diversity (Θ fourfold ), (C) intergenic genetic diversity (Θ Intergenic ), and gene density over 1-Mb nonoverlapping windows in P. tremula (left), P. tremuloides (middle), and P. trichocarpa (right). Gray points represent the statistics computed over 1-Mb nonoverlapping windows. Colored lines denote the lowess curves fit to the two analyzed variables in each species.
Figure Legend Snippet: Correlations of estimates between (A) population-scaled recombination rates ( ρ ), (B) genic genetic diversity (Θ fourfold ), (C) intergenic genetic diversity (Θ Intergenic ), and gene density over 1-Mb nonoverlapping windows in P. tremula (left), P. tremuloides (middle), and P. trichocarpa (right). Gray points represent the statistics computed over 1-Mb nonoverlapping windows. Colored lines denote the lowess curves fit to the two analyzed variables in each species.

Techniques Used:

Genome-wide patterns of polymorphism among three Populus species. Nucleotide diversity (Θ π ) was calculated over 100-kbp nonoverlapping windows in P. tremula (orange line), P. tremuloides (blue line), and P. trichocarpa (green line) along the 19 chromosomes.
Figure Legend Snippet: Genome-wide patterns of polymorphism among three Populus species. Nucleotide diversity (Θ π ) was calculated over 100-kbp nonoverlapping windows in P. tremula (orange line), P. tremuloides (blue line), and P. trichocarpa (green line) along the 19 chromosomes.

Techniques Used: Genome Wide

Distribution and correlations of (A) polymorphism (Θ π ), (B) Tajima’s D , and (C) population-scaled recombination rate (ρ) between pairwise comparisons of P. tremula , P. tremuloides , and P. trichocarpa over 100-kbp nonoverlapping windows. The red-to-yellow-to-blue gradient indicates decreased density of observed events at a given location in the graph. Spearman’s rank correlation coefficient (rho) and the P -value are shown in each subplot. (*** P
Figure Legend Snippet: Distribution and correlations of (A) polymorphism (Θ π ), (B) Tajima’s D , and (C) population-scaled recombination rate (ρ) between pairwise comparisons of P. tremula , P. tremuloides , and P. trichocarpa over 100-kbp nonoverlapping windows. The red-to-yellow-to-blue gradient indicates decreased density of observed events at a given location in the graph. Spearman’s rank correlation coefficient (rho) and the P -value are shown in each subplot. (*** P

Techniques Used:

8) Product Images from "Small RNA Bidirectional Crosstalk During the Interaction Between Wheat and Zymoseptoria tritici"

Article Title: Small RNA Bidirectional Crosstalk During the Interaction Between Wheat and Zymoseptoria tritici

Journal: Frontiers in Plant Science

doi: 10.3389/fpls.2019.01669

Wheat induces small RNAs (sRNAs) to regulate wheat genes as an immune response against Z. tritici . (A) Functions of the wheat genes, which were downregulated and predicted to be targeted by wheat-induced sRNAs. (B – D) Degradome analysis of the wheat genes targeted by miRNA-uniq-133 and miRNA-uniq-113. (E) Relative expression of miRNA-133 and miRNA-113 targeted genes in infections compared to mocks. Each value represents the average of three biological replicates, with three technical replicates per sample. Asterisk indicates significant downregulation during fungal infection ( P value under 0.05).
Figure Legend Snippet: Wheat induces small RNAs (sRNAs) to regulate wheat genes as an immune response against Z. tritici . (A) Functions of the wheat genes, which were downregulated and predicted to be targeted by wheat-induced sRNAs. (B – D) Degradome analysis of the wheat genes targeted by miRNA-uniq-133 and miRNA-uniq-113. (E) Relative expression of miRNA-133 and miRNA-113 targeted genes in infections compared to mocks. Each value represents the average of three biological replicates, with three technical replicates per sample. Asterisk indicates significant downregulation during fungal infection ( P value under 0.05).

Techniques Used: Expressing, Infection

9) Product Images from "CrusTF: a comprehensive resource of transcriptomes for evolutionary and functional studies of crustacean transcription factors"

Article Title: CrusTF: a comprehensive resource of transcriptomes for evolutionary and functional studies of crustacean transcription factors

Journal: BMC Genomics

doi: 10.1186/s12864-017-4305-2

Statistics of CrusTF. a Number of species belonging to 15 orders of Crustacea. b Increase in the number of crustacean species of which transcriptomes or genomes have been published. All four databases belong to National Center for Biotechnology Information (NCBI). SRA Transcriptome: Transcriptomes (RNA-seq) in Short Read Archive; TSA: Transcriptome Shotgun Assembly database; NCBI Genome: NCBI genome database; WGS: Whole Genome Shotgun database. c Number of TFs identified in each species
Figure Legend Snippet: Statistics of CrusTF. a Number of species belonging to 15 orders of Crustacea. b Increase in the number of crustacean species of which transcriptomes or genomes have been published. All four databases belong to National Center for Biotechnology Information (NCBI). SRA Transcriptome: Transcriptomes (RNA-seq) in Short Read Archive; TSA: Transcriptome Shotgun Assembly database; NCBI Genome: NCBI genome database; WGS: Whole Genome Shotgun database. c Number of TFs identified in each species

Techniques Used: RNA Sequencing Assay

10) Product Images from "Full transcription of the chloroplast genome in photosynthetic eukaryotes"

Article Title: Full transcription of the chloroplast genome in photosynthetic eukaryotes

Journal: Scientific Reports

doi: 10.1038/srep30135

Full transcription of the cyanobacteria genomes. ( A – C ) Maps of the cyanobacteria genomes transcription with the outer an d third tracks representing genes in the genome, and the black histogram of the second track represent RNAseq reads mapping (scale log 10 -transformed numbers of sequence reads per nucleotide). ( D ) Comparisons of intergenic and coding region transcription for the five species. Box-and-whisker plots (in which the whiskers denote the 5th and 95th quantiles) of log 2 -transformed numbers of sequence reads per nucleotide are shown for all the intergenic sequences (NonCDS) and coding sequences (CDS). Diamonds represent outliers.
Figure Legend Snippet: Full transcription of the cyanobacteria genomes. ( A – C ) Maps of the cyanobacteria genomes transcription with the outer an d third tracks representing genes in the genome, and the black histogram of the second track represent RNAseq reads mapping (scale log 10 -transformed numbers of sequence reads per nucleotide). ( D ) Comparisons of intergenic and coding region transcription for the five species. Box-and-whisker plots (in which the whiskers denote the 5th and 95th quantiles) of log 2 -transformed numbers of sequence reads per nucleotide are shown for all the intergenic sequences (NonCDS) and coding sequences (CDS). Diamonds represent outliers.

Techniques Used: Transformation Assay, Sequencing, Whisker Assay

11) Product Images from "Insights into the biogenesis and potential functions of exonic circular RNA"

Article Title: Insights into the biogenesis and potential functions of exonic circular RNA

Journal: Scientific Reports

doi: 10.1038/s41598-018-37037-0

Exonic features at human HEK 293 cell circRNA-producing gene loci. ( a ) Relative frequencies of exons by ordinal position N along circRNA-producing genes. Frequency of back-splice ( b ) acceptor and ( c ) donor exon at each position after normalisation to exon frequency as shown in ( a ). *CircRNA acceptor exons were over-represented in the second position of circRNA-producing genes compared to other exon positions (P-value
Figure Legend Snippet: Exonic features at human HEK 293 cell circRNA-producing gene loci. ( a ) Relative frequencies of exons by ordinal position N along circRNA-producing genes. Frequency of back-splice ( b ) acceptor and ( c ) donor exon at each position after normalisation to exon frequency as shown in ( a ). *CircRNA acceptor exons were over-represented in the second position of circRNA-producing genes compared to other exon positions (P-value

Techniques Used: Significance Assay

Selection of human translation candidate (tc-) circRNAs from Transcript Isoform in Polysomes sequencing (TrIP-seq) data. ( a ) UV absorbance profile after separating cycloheximide-treated cytoplasmic HEK 293 cell extract, showing how RNA co-sedimenting with different (poly)ribosomal fractions was collected and sequenced separately. Figure reproduced with modifications, and non-processed sequencing data taken, from the original publication 50 . ( b ) Relative abundance of circRNA (JPM; green) and cognate linear mRNA (RPM; striped) overall for the entire set of HEK circRNAs (left) and across (poly)ribosome co-sedimenting and non-associated (free*; calculated) RNA (right). ( c ) Same as ( b ), but comparing the presence of circRNAs (counts of unique back-spliced junctions) to that of the corresponding cognate linear mRNAs. *’Free’ denotes RNA pool not associated with ribosomes calculated from counts in ribosomal fractions and total cellular RNA as indicated in panel (a) (also see ‘Detection of circRNAs in ribosome sedimentation profiles’ subsection in the Methods for details).
Figure Legend Snippet: Selection of human translation candidate (tc-) circRNAs from Transcript Isoform in Polysomes sequencing (TrIP-seq) data. ( a ) UV absorbance profile after separating cycloheximide-treated cytoplasmic HEK 293 cell extract, showing how RNA co-sedimenting with different (poly)ribosomal fractions was collected and sequenced separately. Figure reproduced with modifications, and non-processed sequencing data taken, from the original publication 50 . ( b ) Relative abundance of circRNA (JPM; green) and cognate linear mRNA (RPM; striped) overall for the entire set of HEK circRNAs (left) and across (poly)ribosome co-sedimenting and non-associated (free*; calculated) RNA (right). ( c ) Same as ( b ), but comparing the presence of circRNAs (counts of unique back-spliced junctions) to that of the corresponding cognate linear mRNAs. *’Free’ denotes RNA pool not associated with ribosomes calculated from counts in ribosomal fractions and total cellular RNA as indicated in panel (a) (also see ‘Detection of circRNAs in ribosome sedimentation profiles’ subsection in the Methods for details).

Techniques Used: Selection, Sequencing, Sedimentation

NET-seq signal values (reflecting inverse Pol II speed across mRNA-coding genes) compared between circRNAs of HEK 293 (green; a , b ) or HeLa (grey; c , d ) cells 52 and the corresponding position-adjusted exons and introns (dark green, white; see ‘Custom reference datasets’ in Methods). ( a , c ) Comparisons among the upstream intron, circRNA exon and downstream intron of single-exon circRNAs (left to right; corresponds to the schematic on top). ( b , d ) Comparisons among the acceptor intron, acceptor exon, internal intron, internal exon, donor exon and donor intron of multi-exon circRNAs (left to right; corresponds to the schematic on top). Asterisks denote significantly different NET-seq signal between the circRNAs and corresponding exon and intron regions in the reference (P-values
Figure Legend Snippet: NET-seq signal values (reflecting inverse Pol II speed across mRNA-coding genes) compared between circRNAs of HEK 293 (green; a , b ) or HeLa (grey; c , d ) cells 52 and the corresponding position-adjusted exons and introns (dark green, white; see ‘Custom reference datasets’ in Methods). ( a , c ) Comparisons among the upstream intron, circRNA exon and downstream intron of single-exon circRNAs (left to right; corresponds to the schematic on top). ( b , d ) Comparisons among the acceptor intron, acceptor exon, internal intron, internal exon, donor exon and donor intron of multi-exon circRNAs (left to right; corresponds to the schematic on top). Asterisks denote significantly different NET-seq signal between the circRNAs and corresponding exon and intron regions in the reference (P-values

Techniques Used:

Patterns of NET-seq signal values (reflecting inverse Pol II speed across mRNA-coding genes) compared between circRNAs and the corresponding position-adjusted exons and introns (see ‘Custom reference datasets’ in Methods) in HEK 293 ( a – c ) and HeLa ( d – f ) cells 52 . NET-seq signals were averaged for different regions of circRNA-producing genes (( a – c ), green line; ( d – f ), grey line) and the corresponding position- and expression-adjusted RefSeq average (( a – c ), green line; ( d – f ), grey line), as depicted in the schematic on top. NET-seq signal values around acceptor are shown with exon 2 acceptors ( a , d ) and with exon 3 or higher acceptors ( b , e ). ( c , f ) Shows NET-seq signal values around internal circRNA exons and donor exons. To better resolve signals, different discontinuous scaling is used on the X-axis. Coverage of the intronic sequences is represented as an average in each position for a 300 nt region, beginning at the adjacent exon (natural scale). Exonic coverage was first scaled to units of exon length and then averaged (justified scale). Regions focussed on the next upstream or downstream exons are also shown. Signal for regions focussed on circRNA-internal exons were averaged across all instances of their type. Boxplots on the top of the chart represent average NET-seq signal (Pol II occupancy) over the respective regions and have the same scale for each cell type and are aligned by zero for all regions except first introns and exons (position- and expression-adjusted RefSeq values for HeLa are shown as white boxes). Asterisks denote significantly different NET-seq signal between the circRNAs and corresponding regions in the reference (P-values
Figure Legend Snippet: Patterns of NET-seq signal values (reflecting inverse Pol II speed across mRNA-coding genes) compared between circRNAs and the corresponding position-adjusted exons and introns (see ‘Custom reference datasets’ in Methods) in HEK 293 ( a – c ) and HeLa ( d – f ) cells 52 . NET-seq signals were averaged for different regions of circRNA-producing genes (( a – c ), green line; ( d – f ), grey line) and the corresponding position- and expression-adjusted RefSeq average (( a – c ), green line; ( d – f ), grey line), as depicted in the schematic on top. NET-seq signal values around acceptor are shown with exon 2 acceptors ( a , d ) and with exon 3 or higher acceptors ( b , e ). ( c , f ) Shows NET-seq signal values around internal circRNA exons and donor exons. To better resolve signals, different discontinuous scaling is used on the X-axis. Coverage of the intronic sequences is represented as an average in each position for a 300 nt region, beginning at the adjacent exon (natural scale). Exonic coverage was first scaled to units of exon length and then averaged (justified scale). Regions focussed on the next upstream or downstream exons are also shown. Signal for regions focussed on circRNA-internal exons were averaged across all instances of their type. Boxplots on the top of the chart represent average NET-seq signal (Pol II occupancy) over the respective regions and have the same scale for each cell type and are aligned by zero for all regions except first introns and exons (position- and expression-adjusted RefSeq values for HeLa are shown as white boxes). Asterisks denote significantly different NET-seq signal between the circRNAs and corresponding regions in the reference (P-values

Techniques Used: Expressing

Linear isoform diversity of human HEK 293 cell circRNA-producing genes. ( a ) mRNA isoform frequency of circRNA-producing genes (green) compared to all human RefSeq genes (dark green). ( b ) Same as ( a ), but compared to exon-count-adjusted genes (dark green). ( c ) Same as ( b ), but compared to gene-length-adjusted genes (dark green). ( d ) Exon counts in circRNA-producing genes compared to RefSeq genes. ( e ) Same as ( d ) but for gene lengths (binned in 20,000 bp steps). ( f – h ) As ( a – c ) but circRNAs are counted as additional transcript isoforms for each gene. Designations and abbreviations as in Fig. 1 . The distributions of data in ( a , d – f and h ) are significantly different between circRNA-producing and reference genes (P-value
Figure Legend Snippet: Linear isoform diversity of human HEK 293 cell circRNA-producing genes. ( a ) mRNA isoform frequency of circRNA-producing genes (green) compared to all human RefSeq genes (dark green). ( b ) Same as ( a ), but compared to exon-count-adjusted genes (dark green). ( c ) Same as ( b ), but compared to gene-length-adjusted genes (dark green). ( d ) Exon counts in circRNA-producing genes compared to RefSeq genes. ( e ) Same as ( d ) but for gene lengths (binned in 20,000 bp steps). ( f – h ) As ( a – c ) but circRNAs are counted as additional transcript isoforms for each gene. Designations and abbreviations as in Fig. 1 . The distributions of data in ( a , d – f and h ) are significantly different between circRNA-producing and reference genes (P-value

Techniques Used: Significance Assay

Exon lengths at human HEK 293 cell circRNA loci. Exons from circRNA-producing genes (green) are compared to RefSeq ( a – c ) or HEK-specific RefSeq ( d , e ) averages in the corresponding linear ordinal positions (dark green). ( a ) Average acceptor exon lengths. ( b ) Same as ( a ), but for donor exons. ( c ) Same as ( a ), but for circRNA-internal exons. ( d ) Single-exon circRNAs (green) compared to the internal exon lengths of HEK-specific RefSeq mRNAs (dark green). ( e ) Same as ( d ), but for acceptor (X1), donor (X2) and internal (X3) exons of multi-exon circRNAs. ( d , e ) Asterisks denote significantly different exon lengths between the circRNA-producing genes and HEK-specific RefSeq mRNAs (P-values
Figure Legend Snippet: Exon lengths at human HEK 293 cell circRNA loci. Exons from circRNA-producing genes (green) are compared to RefSeq ( a – c ) or HEK-specific RefSeq ( d , e ) averages in the corresponding linear ordinal positions (dark green). ( a ) Average acceptor exon lengths. ( b ) Same as ( a ), but for donor exons. ( c ) Same as ( a ), but for circRNA-internal exons. ( d ) Single-exon circRNAs (green) compared to the internal exon lengths of HEK-specific RefSeq mRNAs (dark green). ( e ) Same as ( d ), but for acceptor (X1), donor (X2) and internal (X3) exons of multi-exon circRNAs. ( d , e ) Asterisks denote significantly different exon lengths between the circRNA-producing genes and HEK-specific RefSeq mRNAs (P-values

Techniques Used:

Detection of human and mouse circRNAs in paired-end RNA-seq data 50 , 51 . ( a ) Schematic of the computational pipeline that discards (red ) read pairs that map to the linear transcriptome and identifies pairs where one read maps to a back-spliced junction while the other read maps within the exon span of the putative circRNA (green ). Denotes canonical linear-spliced junction, denotes back-spliced junction. Numbers indicate ‘linear’ ordinal exon position in a gene. ( b ) Numbers of predicted circRNAs (‘junctions’) with ≥0.1 junction per million of reads (JPM), circRNA-producing loci (‘genes’), and related RefSeq mRNA isoforms in MEF cells (blue), mouse heart (MH; red) and HEK 293 cells (green). ( c ) Overlap of circRNA-producing genes between all three sources. ( d ) Overlap of circRNAs identified in the different mouse sources.
Figure Legend Snippet: Detection of human and mouse circRNAs in paired-end RNA-seq data 50 , 51 . ( a ) Schematic of the computational pipeline that discards (red ) read pairs that map to the linear transcriptome and identifies pairs where one read maps to a back-spliced junction while the other read maps within the exon span of the putative circRNA (green ). Denotes canonical linear-spliced junction, denotes back-spliced junction. Numbers indicate ‘linear’ ordinal exon position in a gene. ( b ) Numbers of predicted circRNAs (‘junctions’) with ≥0.1 junction per million of reads (JPM), circRNA-producing loci (‘genes’), and related RefSeq mRNA isoforms in MEF cells (blue), mouse heart (MH; red) and HEK 293 cells (green). ( c ) Overlap of circRNA-producing genes between all three sources. ( d ) Overlap of circRNAs identified in the different mouse sources.

Techniques Used: RNA Sequencing Assay

Intron lengths at human HEK 293 cell circRNA loci. Introns from circRNA-producing genes (green) are compared to RefSeq averages in the corresponding linear ordinal positions (dark green). ( a ) Average intron lengths at the upstream flank of back-spliced acceptor exons. ( b ) Same as ( a ), but for introns at the downstream flank of back-spliced donor exons. ( a , b ) Acceptor and donor introns of circRNA-producing genes are much longer than RefSeq genes in same ordinal positions and overall lengths of acceptor and donor introns were significantly longer than introns of RefSeq genes (measured by P-value
Figure Legend Snippet: Intron lengths at human HEK 293 cell circRNA loci. Introns from circRNA-producing genes (green) are compared to RefSeq averages in the corresponding linear ordinal positions (dark green). ( a ) Average intron lengths at the upstream flank of back-spliced acceptor exons. ( b ) Same as ( a ), but for introns at the downstream flank of back-spliced donor exons. ( a , b ) Acceptor and donor introns of circRNA-producing genes are much longer than RefSeq genes in same ordinal positions and overall lengths of acceptor and donor introns were significantly longer than introns of RefSeq genes (measured by P-value

Techniques Used:

12) Product Images from "Australian human and parrot Chlamydia psittaci strains cluster within the highly virulent 6BC clade of this important zoonotic pathogen"

Article Title: Australian human and parrot Chlamydia psittaci strains cluster within the highly virulent 6BC clade of this important zoonotic pathogen

Journal: Scientific Reports

doi: 10.1038/srep30019

Visual representation of the recombination prediction for all available C. psittaci strains including those isolated from Blue Mountains region of NSW, Australia. The phylogeny of C. psittaci is shown on the left. For each strain the coloured blocks represent the recombination regions identified by Gubbins. Blue blocks are unique to a single isolate while red blocks are shared by multiple strains through common descent. The horizontal position of the blocks represents their position in the whole genome alignment.
Figure Legend Snippet: Visual representation of the recombination prediction for all available C. psittaci strains including those isolated from Blue Mountains region of NSW, Australia. The phylogeny of C. psittaci is shown on the left. For each strain the coloured blocks represent the recombination regions identified by Gubbins. Blue blocks are unique to a single isolate while red blocks are shared by multiple strains through common descent. The horizontal position of the blocks represents their position in the whole genome alignment.

Techniques Used: Isolation

Phylogeny of C. psittaci , including newly described Australian parrot and human C. psittaci strains isolated from a sympatric area of the Blue Mountains region of NSW, Australia. The maximum-likelihood tree was reconstructed with PhyML with the GTR substitution model based on the 172,540 bp alignments of conserved genomic regions. C. psittaci RTH was used as outgroup to root the tree and bootstrap values are shown as percentages. All Australian C. psittaci strains cluster in the 6BC clade.
Figure Legend Snippet: Phylogeny of C. psittaci , including newly described Australian parrot and human C. psittaci strains isolated from a sympatric area of the Blue Mountains region of NSW, Australia. The maximum-likelihood tree was reconstructed with PhyML with the GTR substitution model based on the 172,540 bp alignments of conserved genomic regions. C. psittaci RTH was used as outgroup to root the tree and bootstrap values are shown as percentages. All Australian C. psittaci strains cluster in the 6BC clade.

Techniques Used: Isolation

Bayesian phylogenetic reconstruction and predicted evolutionary divergence times of all the available sequenced C. psittaci isolates from a variety of hosts from different geographical regions. Bayesian evolution rates and divergence times were predicted using BEAST v2.1.3 under the GTR substitution model using a whole genome alignment of 861,327 bp and with tip dates defined as the year of isolation. Strains with an asterisk (*) were sequenced in this study.
Figure Legend Snippet: Bayesian phylogenetic reconstruction and predicted evolutionary divergence times of all the available sequenced C. psittaci isolates from a variety of hosts from different geographical regions. Bayesian evolution rates and divergence times were predicted using BEAST v2.1.3 under the GTR substitution model using a whole genome alignment of 861,327 bp and with tip dates defined as the year of isolation. Strains with an asterisk (*) were sequenced in this study.

Techniques Used: Isolation

13) Product Images from "CrusTF: a comprehensive resource of transcriptomes for evolutionary and functional studies of crustacean transcription factors"

Article Title: CrusTF: a comprehensive resource of transcriptomes for evolutionary and functional studies of crustacean transcription factors

Journal: BMC Genomics

doi: 10.1186/s12864-017-4305-2

Statistics of CrusTF. a Number of species belonging to 15 orders of Crustacea. b Increase in the number of crustacean species of which transcriptomes or genomes have been published. All four databases belong to National Center for Biotechnology Information (NCBI). SRA Transcriptome: Transcriptomes (RNA-seq) in Short Read Archive; TSA: Transcriptome Shotgun Assembly database; NCBI Genome: NCBI genome database; WGS: Whole Genome Shotgun database. c Number of TFs identified in each species
Figure Legend Snippet: Statistics of CrusTF. a Number of species belonging to 15 orders of Crustacea. b Increase in the number of crustacean species of which transcriptomes or genomes have been published. All four databases belong to National Center for Biotechnology Information (NCBI). SRA Transcriptome: Transcriptomes (RNA-seq) in Short Read Archive; TSA: Transcriptome Shotgun Assembly database; NCBI Genome: NCBI genome database; WGS: Whole Genome Shotgun database. c Number of TFs identified in each species

Techniques Used: RNA Sequencing Assay

14) Product Images from "Variation among S-locus haplotypes and among stylar RNases in almond"

Article Title: Variation among S-locus haplotypes and among stylar RNases in almond

Journal: Scientific Reports

doi: 10.1038/s41598-020-57498-6

S -locus structure. Structure of the almond S locus showing the positions of the SLF , S-RNase and SFB genes and long terminal repeat retrotransposons (LTRs). Black lines indicate regions for which sequences were obtained and grey lines indicate gaps in the sequence.
Figure Legend Snippet: S -locus structure. Structure of the almond S locus showing the positions of the SLF , S-RNase and SFB genes and long terminal repeat retrotransposons (LTRs). Black lines indicate regions for which sequences were obtained and grey lines indicate gaps in the sequence.

Techniques Used: Sequencing

15) Product Images from "Full transcription of the chloroplast genome in photosynthetic eukaryotes"

Article Title: Full transcription of the chloroplast genome in photosynthetic eukaryotes

Journal: Scientific Reports

doi: 10.1038/srep30135

Antisense transcription in the chloroplast genome. Strand-specific transcriptome reads showing that antisense transcription (light blue) exceeds sense transcription (light red) for the ndhC gene.
Figure Legend Snippet: Antisense transcription in the chloroplast genome. Strand-specific transcriptome reads showing that antisense transcription (light blue) exceeds sense transcription (light red) for the ndhC gene.

Techniques Used:

Small RNA transcription in the rice chloroplast genome. Small RNA transcriptome reads of four tissues were mapped to the rice plastome. The colored histograms represent small RNA mapping coverage in a logarithmic scale. Detailed statistics of reads mapping is given in Supplementary Table S8 .
Figure Legend Snippet: Small RNA transcription in the rice chloroplast genome. Small RNA transcriptome reads of four tissues were mapped to the rice plastome. The colored histograms represent small RNA mapping coverage in a logarithmic scale. Detailed statistics of reads mapping is given in Supplementary Table S8 .

Techniques Used:

Both strands of the Arabidopsis plastome were transcribed. ( A ) Strand-specific transcriptome reads were mapped to both strands of the Arabidopsis plastome. The outer and third tracks represent genes in the outer and inner strand, respectively. The black histograms of the second and fourth tracks indicate RNAseq reads mapping (scale log 10 -transformed numbers of sequence reads per nucleotide). ( B ) Comparisons of intergenic and coding region transcription for each strand of the Arabidopsis plastome. Box-and-whisker plots (in which the whiskers denote the 5th and 95th quantiles) of log 2 -transformed numbers of sequence reads per nucleotide for all intergenic sequences (NonCDS) and coding sequences (CDS). Diamonds represent outliers.
Figure Legend Snippet: Both strands of the Arabidopsis plastome were transcribed. ( A ) Strand-specific transcriptome reads were mapped to both strands of the Arabidopsis plastome. The outer and third tracks represent genes in the outer and inner strand, respectively. The black histograms of the second and fourth tracks indicate RNAseq reads mapping (scale log 10 -transformed numbers of sequence reads per nucleotide). ( B ) Comparisons of intergenic and coding region transcription for each strand of the Arabidopsis plastome. Box-and-whisker plots (in which the whiskers denote the 5th and 95th quantiles) of log 2 -transformed numbers of sequence reads per nucleotide for all intergenic sequences (NonCDS) and coding sequences (CDS). Diamonds represent outliers.

Techniques Used: Transformation Assay, Sequencing, Whisker Assay

Complete cp genomes were de novo assembled from transcriptome data. The wrap sequence alignment of the assembled genome. The black blocks depict genome similarity for these species. A detailed species list is provided in Supplementary Table S7 .
Figure Legend Snippet: Complete cp genomes were de novo assembled from transcriptome data. The wrap sequence alignment of the assembled genome. The black blocks depict genome similarity for these species. A detailed species list is provided in Supplementary Table S7 .

Techniques Used: Sequencing

16) Product Images from "Comparative Temporal Transcriptome Profiling of Wheat near Isogenic Line Carrying Lr57 under Compatible and Incompatible Interactions"

Article Title: Comparative Temporal Transcriptome Profiling of Wheat near Isogenic Line Carrying Lr57 under Compatible and Incompatible Interactions

Journal: Frontiers in Plant Science

doi: 10.3389/fpls.2016.01943

Co-regulated genes expression network of highly expressed transcription factor with other resistance genes . Hexagon represents the transcription factors with more than 20 connections with nearby genes and circle represents the resistance gene, peroxidases, glucanases, cytochrome P450, ABC transporters, Phenylalanine ammonia lyase, protein kinases and O-methyltransferase. Edges represents the degree of connectivity in depicted by weighted gene matrix. (A) Gene network from cluster 1 of WL711. (B) Gene network from cluster 1 of WL711+ Lr 57.
Figure Legend Snippet: Co-regulated genes expression network of highly expressed transcription factor with other resistance genes . Hexagon represents the transcription factors with more than 20 connections with nearby genes and circle represents the resistance gene, peroxidases, glucanases, cytochrome P450, ABC transporters, Phenylalanine ammonia lyase, protein kinases and O-methyltransferase. Edges represents the degree of connectivity in depicted by weighted gene matrix. (A) Gene network from cluster 1 of WL711. (B) Gene network from cluster 1 of WL711+ Lr 57.

Techniques Used: Expressing

MapMan visualization of defense response in WL711+ Lr 57 after pathogen attack. DEGs (fold changes ≥ 2, p ≤ 0.05) were imported into MapMan . Up- and Down-regulated DEGs are represented with blue and red squares, respectively with log2 transformed values.
Figure Legend Snippet: MapMan visualization of defense response in WL711+ Lr 57 after pathogen attack. DEGs (fold changes ≥ 2, p ≤ 0.05) were imported into MapMan . Up- and Down-regulated DEGs are represented with blue and red squares, respectively with log2 transformed values.

Techniques Used: Transformation Assay

17) Product Images from "Asymmetric Context-Dependent Mutation Patterns Revealed through Mutation–Accumulation Experiments"

Article Title: Asymmetric Context-Dependent Mutation Patterns Revealed through Mutation–Accumulation Experiments

Journal: Molecular Biology and Evolution

doi: 10.1093/molbev/msv055

Rate and spectrum of base-substitution mutations in WT and MMR – Bacillus subtilis MA lines. A–B . Distribution of base substitutions in 50 WT and 19 MMR – B. subtilis MA lines. From the outer ring to inner ring scaled to genome size:
Figure Legend Snippet: Rate and spectrum of base-substitution mutations in WT and MMR – Bacillus subtilis MA lines. A–B . Distribution of base substitutions in 50 WT and 19 MMR – B. subtilis MA lines. From the outer ring to inner ring scaled to genome size:

Techniques Used:

18) Product Images from "High-throughput sequencing data and antibiotic resistance mechanisms of soil microbial communities in non-irrigated and irrigated soils with raw sewage in African cities"

Article Title: High-throughput sequencing data and antibiotic resistance mechanisms of soil microbial communities in non-irrigated and irrigated soils with raw sewage in African cities

Journal: Data in Brief

doi: 10.1016/j.dib.2019.104638

Mechanisms of antibiotic resistance (%) of the antibiotic resistance genes (based on their abundance) derived from the metagenomic reads in (a) irrigated fields and (b) non-irrigated fields (n = 3).
Figure Legend Snippet: Mechanisms of antibiotic resistance (%) of the antibiotic resistance genes (based on their abundance) derived from the metagenomic reads in (a) irrigated fields and (b) non-irrigated fields (n = 3).

Techniques Used: Derivative Assay

19) Product Images from "An Indel Polymorphism in the MtnA 3' Untranslated Region Is Associated with Gene Expression Variation and Local Adaptation in Drosophila melanogaster"

Article Title: An Indel Polymorphism in the MtnA 3' Untranslated Region Is Associated with Gene Expression Variation and Local Adaptation in Drosophila melanogaster

Journal: PLoS Genetics

doi: 10.1371/journal.pgen.1005987

Association between an indel polymorphism in the MtnA 3' UTR and gene expression variation. (A) An indel (and a linked SNP marked in gray) in the MtnA 3' UTR are the only polymorphisms within the 6-kb MtnA region that show a large difference in frequency between an African and a European population of D . melanogaster . A comparison with three outgroup species, D . sechellia (Sec), D . simulans (Sim) and D . yakuba (Yak), indicated that the deletion is the derived variant. (B) MtnA expression in the brain and the gut of eight European (NL) lines, shown in blue, and eight African (ZK) lines, shown in green. The two European lines lacking the deletion, NL11 and NL15 , show lower MtnA expression than those with the deletion.
Figure Legend Snippet: Association between an indel polymorphism in the MtnA 3' UTR and gene expression variation. (A) An indel (and a linked SNP marked in gray) in the MtnA 3' UTR are the only polymorphisms within the 6-kb MtnA region that show a large difference in frequency between an African and a European population of D . melanogaster . A comparison with three outgroup species, D . sechellia (Sec), D . simulans (Sim) and D . yakuba (Yak), indicated that the deletion is the derived variant. (B) MtnA expression in the brain and the gut of eight European (NL) lines, shown in blue, and eight African (ZK) lines, shown in green. The two European lines lacking the deletion, NL11 and NL15 , show lower MtnA expression than those with the deletion.

Techniques Used: Expressing, Size-exclusion Chromatography, Derivative Assay, Variant Assay

Evidence for positive selection at the MtnA locus. (A) Watterson’s θ of D . melanogaster populations from Zimbabwe (ZK), the Netherlands (NL) and Sweden (SU) calculated in sliding windows of 500 bp with a step size of 250 bp. (B) F st values for pairwise comparisons of ZK, NL and SU calculated in sliding windows of 500 bp with a step size of 250 bp. (C) Selective sweep (SweepFinder) analysis of the Netherlands population showing the composite likelihood ratio (CLR) statistic in sliding windows of 1000 bp. (D) Selective sweep ( SweepFinder ) analysis of the Swedish population showing the CLR statistic in sliding windows of 1000 bp. The black line indicates the 5% significance threshold calculated using the demographic model of Duchen et al. [ 5 ] for neutral simulations. The red line indicates the 5% significance threshold calculated using the demographic model of Werzner et al. [ 6 ] for neutral simulations and the gray dashed line indicates the 5% significance threshold using the model of Thornton and Andolfatto [ 35 ]. (E) Gene models for the 6-kb region analyzed. The gray highlighted region indicates the position of the 49-bp indel polymorphism in the MtnA 3’ UTR.
Figure Legend Snippet: Evidence for positive selection at the MtnA locus. (A) Watterson’s θ of D . melanogaster populations from Zimbabwe (ZK), the Netherlands (NL) and Sweden (SU) calculated in sliding windows of 500 bp with a step size of 250 bp. (B) F st values for pairwise comparisons of ZK, NL and SU calculated in sliding windows of 500 bp with a step size of 250 bp. (C) Selective sweep (SweepFinder) analysis of the Netherlands population showing the composite likelihood ratio (CLR) statistic in sliding windows of 1000 bp. (D) Selective sweep ( SweepFinder ) analysis of the Swedish population showing the CLR statistic in sliding windows of 1000 bp. The black line indicates the 5% significance threshold calculated using the demographic model of Duchen et al. [ 5 ] for neutral simulations. The red line indicates the 5% significance threshold calculated using the demographic model of Werzner et al. [ 6 ] for neutral simulations and the gray dashed line indicates the 5% significance threshold using the model of Thornton and Andolfatto [ 35 ]. (E) Gene models for the 6-kb region analyzed. The gray highlighted region indicates the position of the 49-bp indel polymorphism in the MtnA 3’ UTR.

Techniques Used: Selection

Reporter gene constructs and their expression. (A) The gray boxes represent the MtnA promoter, which is identical between the African and European alleles. The white boxes represent the GFP/ lacZ reporter genes. The blue hatched box represents the MtnA 3’ UTR with the deletion. The green box represents the MtnA 3’ UTR with the additional 49 bp marked in red. The same color scheme applies to the bar plots. (B) The two versions of the GFP reporter gene differ significantly in expression in heads ( t -test, P = 0.0019) and bodies ( t -test, P = 0.0046), as assayed by qRT-PCR. (C) The two versions of the lacZ reporter gene differed significantly in expression in heads ( t -test, P = 0.0006) and guts ( t -test, P = 0.0001) as measured by β-galactosidase enzymatic activity. The error bars represent the standard error of the mean.
Figure Legend Snippet: Reporter gene constructs and their expression. (A) The gray boxes represent the MtnA promoter, which is identical between the African and European alleles. The white boxes represent the GFP/ lacZ reporter genes. The blue hatched box represents the MtnA 3’ UTR with the deletion. The green box represents the MtnA 3’ UTR with the additional 49 bp marked in red. The same color scheme applies to the bar plots. (B) The two versions of the GFP reporter gene differ significantly in expression in heads ( t -test, P = 0.0019) and bodies ( t -test, P = 0.0046), as assayed by qRT-PCR. (C) The two versions of the lacZ reporter gene differed significantly in expression in heads ( t -test, P = 0.0006) and guts ( t -test, P = 0.0001) as measured by β-galactosidase enzymatic activity. The error bars represent the standard error of the mean.

Techniques Used: Construct, Expressing, Quantitative RT-PCR, Activity Assay

Proportional mortality after oxidative stress. (A) RNAi-mediated MtnA knockdown (hatched lines) and control flies (solid lines). P -values are shown for within population/background comparisons. (B) Dutch (blue) and Malaysian (orange) flies with the deletion (hatched lines) and without the deletion (solid lines) in the MtnA 3’ UTR. Error bars indicate the standard error of the mean. * P
Figure Legend Snippet: Proportional mortality after oxidative stress. (A) RNAi-mediated MtnA knockdown (hatched lines) and control flies (solid lines). P -values are shown for within population/background comparisons. (B) Dutch (blue) and Malaysian (orange) flies with the deletion (hatched lines) and without the deletion (solid lines) in the MtnA 3’ UTR. Error bars indicate the standard error of the mean. * P

Techniques Used:

Expression of an MtnA -GFP reporter gene in the brain. (A-C) GFP expression driven by the reporter gene construct with the ancestral MtnA 3’ UTR variant. (D-G) Higher magnification of the brain regions where GFP is expressed. AL: antennal lobe, MB: mushroom bodies, SOG: subesophageal ganglion, Lo: lobula, Me: medulla. In (G) the arrow indicates cells expressing GFP. Green: GFP, red: anti-disclarge, targeting general neuropil.
Figure Legend Snippet: Expression of an MtnA -GFP reporter gene in the brain. (A-C) GFP expression driven by the reporter gene construct with the ancestral MtnA 3’ UTR variant. (D-G) Higher magnification of the brain regions where GFP is expressed. AL: antennal lobe, MB: mushroom bodies, SOG: subesophageal ganglion, Lo: lobula, Me: medulla. In (G) the arrow indicates cells expressing GFP. Green: GFP, red: anti-disclarge, targeting general neuropil.

Techniques Used: Expressing, Construct, Variant Assay

20) Product Images from "Genomic Analysis of Salmonella enterica Serovar Typhimurium Characterizes Strain Diversity for Recent U.S. Salmonellosis Cases and Identifies Mutations Linked to Loss of Fitness under Nitrosative and Oxidative Stress"

Article Title: Genomic Analysis of Salmonella enterica Serovar Typhimurium Characterizes Strain Diversity for Recent U.S. Salmonellosis Cases and Identifies Mutations Linked to Loss of Fitness under Nitrosative and Oxidative Stress

Journal: mBio

doi: 10.1128/mBio.00154-16

Subclade 1a S . Typhimurium with the C667T mutation in HmpA shows impaired growth under nitrosative stress. Growth curves for strains BC_2558 and SOHS02-20, representing subclade 1a strains, strain 14028S (wild type), and the hmp null strain ( hmpA mutant) in the presence and absence of the NO donor, SNAC. The values are means ± standard deviations (error bars) for the three independent trials.
Figure Legend Snippet: Subclade 1a S . Typhimurium with the C667T mutation in HmpA shows impaired growth under nitrosative stress. Growth curves for strains BC_2558 and SOHS02-20, representing subclade 1a strains, strain 14028S (wild type), and the hmp null strain ( hmpA mutant) in the presence and absence of the NO donor, SNAC. The values are means ± standard deviations (error bars) for the three independent trials.

Techniques Used: Mutagenesis

S . Typhimurium with nsSNPs in tetrathionate respiration genes show no growth impairment when cultivated anaerobically. Strain LT2 (wild type) and four S . Typhimurium strains with amino acid substitutions in TtrC or TtrS were grown anaerobically in BBL tetrathionate broth: strain 14028S (TtrC R187H) and BC_2558, SOHS02-68 and SOHS02-20 (TtrC R187H, TtrS V421G, D204A). The number of CFU were determined at 0 and 24 h. The values are the means plus standard deviations (error bars) of the ratio between the number of CFU at 24 h and the initial CFU count for each strain.
Figure Legend Snippet: S . Typhimurium with nsSNPs in tetrathionate respiration genes show no growth impairment when cultivated anaerobically. Strain LT2 (wild type) and four S . Typhimurium strains with amino acid substitutions in TtrC or TtrS were grown anaerobically in BBL tetrathionate broth: strain 14028S (TtrC R187H) and BC_2558, SOHS02-68 and SOHS02-20 (TtrC R187H, TtrS V421G, D204A). The number of CFU were determined at 0 and 24 h. The values are the means plus standard deviations (error bars) of the ratio between the number of CFU at 24 h and the initial CFU count for each strain.

Techniques Used:

S . Typhimurium core gene phylogeny. Maximum likelihood phylogeny of 56 S . Typhimurium strains relative to the S . Saintpaul SARA23 outgroup. S . Saintpaul SARA23 was used to root the tree but was removed in order to view branch topologies among the S . Typhimurium strains. The three basal clades are labeled 1 to 3, and seven clade 1 subclades are labeled 1a to 1g. Collection location and year in bold type follow strain names and are abbreviated as follows: DC, Democratic Republic of the Congo; JP, Japan; MW, Malawi; MX, Mexico; MZ, Mozambique; UK, United Kingdom; US, United States. Strains with unknown location and year have no abbreviations. Strains from the CDC collected between 2000 and 2010 are labeled “US10.” Strain names for animal isolates are boxed. BAPS groups are color coded and named in a manner consistent with Table 1 . Branches with 100% bootstrap support are labeled with an asterisk.
Figure Legend Snippet: S . Typhimurium core gene phylogeny. Maximum likelihood phylogeny of 56 S . Typhimurium strains relative to the S . Saintpaul SARA23 outgroup. S . Saintpaul SARA23 was used to root the tree but was removed in order to view branch topologies among the S . Typhimurium strains. The three basal clades are labeled 1 to 3, and seven clade 1 subclades are labeled 1a to 1g. Collection location and year in bold type follow strain names and are abbreviated as follows: DC, Democratic Republic of the Congo; JP, Japan; MW, Malawi; MX, Mexico; MZ, Mozambique; UK, United Kingdom; US, United States. Strains with unknown location and year have no abbreviations. Strains from the CDC collected between 2000 and 2010 are labeled “US10.” Strain names for animal isolates are boxed. BAPS groups are color coded and named in a manner consistent with Table 1 . Branches with 100% bootstrap support are labeled with an asterisk.

Techniques Used: Labeling

Subclade 1a S . Typhimurium with E117G mutation in KatE are deficient in KatE catalase activity. (A) Cellular extracts for eight strains were run individually in a nondenaturing polyacrylamide gel, and the catalase activity was visualized by the method of Woodbury et al. ( 43 ). This method relies on the reduction of potassium ferricyanide(III) to potassium ferrocyanide(II) in the presence of hydrogen peroxide, which upon reaction with ferric chloride forms a stable, insoluble Prussian blue pigment. A clear zone is present in regions of the gel that contain catalase activity. (B) Stationary-phase cultures of eight strains were mixed with equal volumes of Triton X-100 and 30% hydrogen peroxide to assay global catalase activity. The formation of oxygen bubbles is apparent in wild-type strains 14028S, LT2, and SL1344 and in strains with the D606G (DT104, BC_2557) and Q45K (ST34) mutations in KatE. Bubble formation is relatively reduced in strains BC_2558 and SOHS02-20 with the E117G mutation.
Figure Legend Snippet: Subclade 1a S . Typhimurium with E117G mutation in KatE are deficient in KatE catalase activity. (A) Cellular extracts for eight strains were run individually in a nondenaturing polyacrylamide gel, and the catalase activity was visualized by the method of Woodbury et al. ( 43 ). This method relies on the reduction of potassium ferricyanide(III) to potassium ferrocyanide(II) in the presence of hydrogen peroxide, which upon reaction with ferric chloride forms a stable, insoluble Prussian blue pigment. A clear zone is present in regions of the gel that contain catalase activity. (B) Stationary-phase cultures of eight strains were mixed with equal volumes of Triton X-100 and 30% hydrogen peroxide to assay global catalase activity. The formation of oxygen bubbles is apparent in wild-type strains 14028S, LT2, and SL1344 and in strains with the D606G (DT104, BC_2557) and Q45K (ST34) mutations in KatE. Bubble formation is relatively reduced in strains BC_2558 and SOHS02-20 with the E117G mutation.

Techniques Used: Mutagenesis, Activity Assay

21) Product Images from "IsdB-dependent Hemoglobin Binding Is Required for Acquisition of Heme by Staphylococcus aureus"

Article Title: IsdB-dependent Hemoglobin Binding Is Required for Acquisition of Heme by Staphylococcus aureus

Journal: The Journal of Infectious Diseases

doi: 10.1093/infdis/jit817

IsdB polymorphisms across Staphylococcus aureus strains. A , Hotspots of polymorphisms in the isdB gene as revealed by the analysis of 3,277 S. aureus strains from the NCBI SRA database compared to N315 reference genome. B , Frequency distribution of all
Figure Legend Snippet: IsdB polymorphisms across Staphylococcus aureus strains. A , Hotspots of polymorphisms in the isdB gene as revealed by the analysis of 3,277 S. aureus strains from the NCBI SRA database compared to N315 reference genome. B , Frequency distribution of all

Techniques Used:

22) Product Images from "Mobile genetic element insertions drive antibiotic resistance across pathogens"

Article Title: Mobile genetic element insertions drive antibiotic resistance across pathogens

Journal: bioRxiv

doi: 10.1101/527788

A new approach to identify MGEs from short-read sequencing data. a , A schematic representation of the workflow implemented in this study. The analysis requires a reference genome of a given species and short-read sequencing FASTQ files as input. The reads are aligned to the provided reference genome and assembled using third-party software. Candidate MGE insertion sites are identified from the alignment to the reference using our own software suite, called mustache . This approach identifies sites where oppositely-oriented clipped read ends are found within 20 bases of each other. Consensus sequences of these flanking ends are then identified, with the assumption being that they represent the flanks of the inserted element. The intervening sequence between the candidate flanks is inferred by aligning flanks to the assembled genome, a reference genome, and our dynamically constructed reference database of all identified MGEs. b , The inference method used to characterize the inserted elements of the downloaded data. “Inferred from assembly with full context” indicates that the sequence was found in the expected sequence context within the assembly and is considered one of the highest-confidence inferred sequences. “Inferred from assembly with half context” indicates that the sequence was found in the expected sequence context on one end of the inserted element, and the other element was truncated at the end of a partially assembled contig. “Inferred from overlap” indicates that the sequence was recovered simply by finding an overlap of two paired flanks. Very few elements are recovered by this method, as we are limiting our analysis to only elements greater than 300 base pairs in length. “Inferred from assembly without context” indicates that the sequence identified was recovered from the assembly, but not within the expected sequence context, presumably due to assembly errors. “Inferred from dynamically-constructed database” refers to elements that were not recovered from the assembly but were recovered from the reference genome or from our dynamically constructed database. The database in this case is built from the accumulated inferred sequences found in the assembly and in the reference across all sequenced isolates. “Ambiguous identity - Resolved” indicates that the element was initially is assigned to multiple element clusters but was resolved using several techniques described in the methods. “Ambiguous identity - Unresolved” indicates the the inserted element maps to multiple element clusters and could not be resolved. This excludes these insertions from some of the downstream analyses. c, Results of simulations using the mustache software tools. We simulated insertions into the nine species analyzed in this study. Reference genomes were mutated with base pair substitutions and short indels at a rate of 0.085 mutations per base pair. An insertion is considered found if both of its flanks are recovered near the expected insertion seite, properly paired with each other, and the consensus flanks show high similarity with the expected inserted sequence. Precision indicates the proportion of reported results that are true simulated MGE insertions, and sensitivity indicates the proportion of simulated MGE insertions that are recovered by mustache . d , An analysis of the proportion of elements identified in the mustache workflow. A “unique element” refers to a unique cluster of elements that are 95% similar across 85% of their respective sequences. The number of elements predicted to be IS elements is shown in purple. “MGE w/ passenger genes” in blue indicates other elements that contain both predicted transposases and one or more passenger genes. “Contains CDS” in green indicates all other elements that contain a predicted CDS, but no transposase. “Other” in yellow indicates all other inserted elements that contain no predicted CDS. e-g, Schematic representations of the many ways that MGEs influence biological processes: e , through carrying cargo proteins of specific function. f, through disrupting functional genomic elements, and g , by introducing outwardly-directed promoters, causing up-regulation of adjacent genes. The MGE insertions depicted in ( f ) affect intergenic regulatory elements, such as (R)epressors and (P)romoters, the coding sequence itself, and regions downstream of coding sequences. Blue arrow indicates a probable gain-of-function MGE insertion causing greater expression of the respective gene. Red arrows indicate probable loss-of-function MGE insertion. Grey arrows indicate mutations of unknown function but are likely to be neutral.
Figure Legend Snippet: A new approach to identify MGEs from short-read sequencing data. a , A schematic representation of the workflow implemented in this study. The analysis requires a reference genome of a given species and short-read sequencing FASTQ files as input. The reads are aligned to the provided reference genome and assembled using third-party software. Candidate MGE insertion sites are identified from the alignment to the reference using our own software suite, called mustache . This approach identifies sites where oppositely-oriented clipped read ends are found within 20 bases of each other. Consensus sequences of these flanking ends are then identified, with the assumption being that they represent the flanks of the inserted element. The intervening sequence between the candidate flanks is inferred by aligning flanks to the assembled genome, a reference genome, and our dynamically constructed reference database of all identified MGEs. b , The inference method used to characterize the inserted elements of the downloaded data. “Inferred from assembly with full context” indicates that the sequence was found in the expected sequence context within the assembly and is considered one of the highest-confidence inferred sequences. “Inferred from assembly with half context” indicates that the sequence was found in the expected sequence context on one end of the inserted element, and the other element was truncated at the end of a partially assembled contig. “Inferred from overlap” indicates that the sequence was recovered simply by finding an overlap of two paired flanks. Very few elements are recovered by this method, as we are limiting our analysis to only elements greater than 300 base pairs in length. “Inferred from assembly without context” indicates that the sequence identified was recovered from the assembly, but not within the expected sequence context, presumably due to assembly errors. “Inferred from dynamically-constructed database” refers to elements that were not recovered from the assembly but were recovered from the reference genome or from our dynamically constructed database. The database in this case is built from the accumulated inferred sequences found in the assembly and in the reference across all sequenced isolates. “Ambiguous identity - Resolved” indicates that the element was initially is assigned to multiple element clusters but was resolved using several techniques described in the methods. “Ambiguous identity - Unresolved” indicates the the inserted element maps to multiple element clusters and could not be resolved. This excludes these insertions from some of the downstream analyses. c, Results of simulations using the mustache software tools. We simulated insertions into the nine species analyzed in this study. Reference genomes were mutated with base pair substitutions and short indels at a rate of 0.085 mutations per base pair. An insertion is considered found if both of its flanks are recovered near the expected insertion seite, properly paired with each other, and the consensus flanks show high similarity with the expected inserted sequence. Precision indicates the proportion of reported results that are true simulated MGE insertions, and sensitivity indicates the proportion of simulated MGE insertions that are recovered by mustache . d , An analysis of the proportion of elements identified in the mustache workflow. A “unique element” refers to a unique cluster of elements that are 95% similar across 85% of their respective sequences. The number of elements predicted to be IS elements is shown in purple. “MGE w/ passenger genes” in blue indicates other elements that contain both predicted transposases and one or more passenger genes. “Contains CDS” in green indicates all other elements that contain a predicted CDS, but no transposase. “Other” in yellow indicates all other inserted elements that contain no predicted CDS. e-g, Schematic representations of the many ways that MGEs influence biological processes: e , through carrying cargo proteins of specific function. f, through disrupting functional genomic elements, and g , by introducing outwardly-directed promoters, causing up-regulation of adjacent genes. The MGE insertions depicted in ( f ) affect intergenic regulatory elements, such as (R)epressors and (P)romoters, the coding sequence itself, and regions downstream of coding sequences. Blue arrow indicates a probable gain-of-function MGE insertion causing greater expression of the respective gene. Red arrows indicate probable loss-of-function MGE insertion. Grey arrows indicate mutations of unknown function but are likely to be neutral.

Techniques Used: Sequencing, Software, Construct, Functional Assay, Expressing

23) Product Images from "Bioinformatic identification and expression analysis of Nelumbo nucifera microRNA and their targets 1"

Article Title: Bioinformatic identification and expression analysis of Nelumbo nucifera microRNA and their targets 1

Journal: Applications in Plant Sciences

doi: 10.3732/apps.1500046

Several miRNA-5p/miRNA-3p secondary structures in Nelumbo nucifera . (A) Nnu-miR156c-5p/3p; (B) Nnu-miR169c-5p/3p; (C) Nnu-miR390a-5p/3p; (D) Nnu-miR396b-5p/3p.
Figure Legend Snippet: Several miRNA-5p/miRNA-3p secondary structures in Nelumbo nucifera . (A) Nnu-miR156c-5p/3p; (B) Nnu-miR169c-5p/3p; (C) Nnu-miR390a-5p/3p; (D) Nnu-miR396b-5p/3p.

Techniques Used:

Sense and antisense miRNAs and their secondary structures in Nelumbo nucifera .
Figure Legend Snippet: Sense and antisense miRNAs and their secondary structures in Nelumbo nucifera .

Techniques Used:

The relative expression levels of five miRNAs and target genes in young leaves, stems, and flowers of Nelumbo nucifera . (A) The relative expression levels of five miRNAs in N. nucifera . (B) The relative expression levels of five corresponding target genes in N. nucifera . Significant differences of the differential expression among different tissues in N. nucifera were evaluated by Student’s t test (* P
Figure Legend Snippet: The relative expression levels of five miRNAs and target genes in young leaves, stems, and flowers of Nelumbo nucifera . (A) The relative expression levels of five miRNAs in N. nucifera . (B) The relative expression levels of five corresponding target genes in N. nucifera . Significant differences of the differential expression among different tissues in N. nucifera were evaluated by Student’s t test (* P

Techniques Used: Expressing

The relative expression levels of five miRNAs in young leaves, stems, and flowers of Nelumbo nucifera . Significant differences of the differential expression among different tissues in N. nucifera were evaluated by Student’s t test (* P
Figure Legend Snippet: The relative expression levels of five miRNAs in young leaves, stems, and flowers of Nelumbo nucifera . Significant differences of the differential expression among different tissues in N. nucifera were evaluated by Student’s t test (* P

Techniques Used: Expressing

Distribution of Nelumbo nucifera mature miRNA lengths (A) and pre-miRNA lengths (B).
Figure Legend Snippet: Distribution of Nelumbo nucifera mature miRNA lengths (A) and pre-miRNA lengths (B).

Techniques Used:

Workflow for identifying potential miRNAs in Nelumbo nucifera .
Figure Legend Snippet: Workflow for identifying potential miRNAs in Nelumbo nucifera .

Techniques Used:

24) Product Images from "Variation among S-locus haplotypes and among stylar RNases in almond"

Article Title: Variation among S-locus haplotypes and among stylar RNases in almond

Journal: Scientific Reports

doi: 10.1038/s41598-020-57498-6

S -locus structure. Structure of the almond S locus showing the positions of the SLF , S-RNase and SFB genes and long terminal repeat retrotransposons (LTRs). Black lines indicate regions for which sequences were obtained and grey lines indicate gaps in the sequence.
Figure Legend Snippet: S -locus structure. Structure of the almond S locus showing the positions of the SLF , S-RNase and SFB genes and long terminal repeat retrotransposons (LTRs). Black lines indicate regions for which sequences were obtained and grey lines indicate gaps in the sequence.

Techniques Used: Sequencing

25) Product Images from "Comparative Transcriptome Analysis Reveals Hormone Signaling Genes Involved in the Launch of Culm-Shape Differentiation in Dendrocalamus sinicus"

Article Title: Comparative Transcriptome Analysis Reveals Hormone Signaling Genes Involved in the Launch of Culm-Shape Differentiation in Dendrocalamus sinicus

Journal: Genes

doi: 10.3390/genes9010004

Overview of the serial analysis of differentially expressed genes (DEGs) identified by pairwise comparisons of the six transcriptomes: SC5, SC15, SC30, BC5, BC15, and BC30. ( a ) Venn diagram of the DEGs in bent culm (BC) at the three stages; ( b ) Venn diagram of the DEGs in straight culm (SC) at the three stages; ( c ) Venn diagram of the DEGs between BC and SC at the three stages.
Figure Legend Snippet: Overview of the serial analysis of differentially expressed genes (DEGs) identified by pairwise comparisons of the six transcriptomes: SC5, SC15, SC30, BC5, BC15, and BC30. ( a ) Venn diagram of the DEGs in bent culm (BC) at the three stages; ( b ) Venn diagram of the DEGs in straight culm (SC) at the three stages; ( c ) Venn diagram of the DEGs between BC and SC at the three stages.

Techniques Used:

Heatmap of differentially expressed genes assigned to hormone signal transduction pathways in the six D. sinicus transcriptomes: BC5, BC15, BC30, SC5, SC15, and SC30. DEGs related to ( a ) auxin, ( b ) ethylene, and ( c ) abscisic acid. FPKM (fragments per kilobase of exon per million mapped reads) values range from 0 to 50.
Figure Legend Snippet: Heatmap of differentially expressed genes assigned to hormone signal transduction pathways in the six D. sinicus transcriptomes: BC5, BC15, BC30, SC5, SC15, and SC30. DEGs related to ( a ) auxin, ( b ) ethylene, and ( c ) abscisic acid. FPKM (fragments per kilobase of exon per million mapped reads) values range from 0 to 50.

Techniques Used: Transduction

Expression of 10 selected genes as determined by qRT-PCR in comparison with the transcriptome results. The qRT-PCR values for each gene are the means ± SD of three biological replicates, with three technical replicates per experiment. The gene names and primers used for qRT-PCR analysis are shown in Table 1 . The white bars indicate FPKM values as determined by transcriptome sequencing, and the grey bars show the expression as determined by qRT-PCR. ASR : abscisic acid stress ripening protein; EIN3 : ethylene-insensitive protein 3; APR 12 . 5 kDa : auxin-repressed 12.5 kDa protein-like; IAA17 : auxin-responsive protein IAA17-like; IAA21 : auxin-responsive protein IAA21; CAD : cinnamyl–alcohol dehydrogenase; 4CL : 4-coumarate–CoA ligase; CCoAOMT : caffeoyl–CoA O -methyltransferase; PTAL : phenylalanine/tyrosine ammonia-lyase.
Figure Legend Snippet: Expression of 10 selected genes as determined by qRT-PCR in comparison with the transcriptome results. The qRT-PCR values for each gene are the means ± SD of three biological replicates, with three technical replicates per experiment. The gene names and primers used for qRT-PCR analysis are shown in Table 1 . The white bars indicate FPKM values as determined by transcriptome sequencing, and the grey bars show the expression as determined by qRT-PCR. ASR : abscisic acid stress ripening protein; EIN3 : ethylene-insensitive protein 3; APR 12 . 5 kDa : auxin-repressed 12.5 kDa protein-like; IAA17 : auxin-responsive protein IAA17-like; IAA21 : auxin-responsive protein IAA21; CAD : cinnamyl–alcohol dehydrogenase; 4CL : 4-coumarate–CoA ligase; CCoAOMT : caffeoyl–CoA O -methyltransferase; PTAL : phenylalanine/tyrosine ammonia-lyase.

Techniques Used: Expressing, Quantitative RT-PCR, Sequencing

Expression patterns of the expressed genes assigned to lignin biosynthesis in the six D. sinicus transcriptomes: BC5, BC15, BC30, SC5, SC15, and SC30. Completed according to KEGG source record: ko00940. All metabolic enzymes predicted in the D. sinicus transcriptome are marked in the pathway. FPKM values range from 0 to 200. PAL: phenylalanine ammonia-lyase; PTAL: phenylalanine/tyrosine ammonia-lyase; C4H: cinnamate 4-hydroxylase; 4CL: 4-coumarate–CoA ligase; HCT: shikimate O -hydroxycinnamoyltransferase; C3′H: coumaroylquinate(coumaroylshikimate)3′-monooxygenase; CCoAOMT: caffeoyl-CoA O -methyltransferase; CCR: cinnamoyl–CoA reductase, CAD: cinnamyl–alcohol dehydrogenase; F5H: ferulate-5-hydroxylase; POD: peroxidase.
Figure Legend Snippet: Expression patterns of the expressed genes assigned to lignin biosynthesis in the six D. sinicus transcriptomes: BC5, BC15, BC30, SC5, SC15, and SC30. Completed according to KEGG source record: ko00940. All metabolic enzymes predicted in the D. sinicus transcriptome are marked in the pathway. FPKM values range from 0 to 200. PAL: phenylalanine ammonia-lyase; PTAL: phenylalanine/tyrosine ammonia-lyase; C4H: cinnamate 4-hydroxylase; 4CL: 4-coumarate–CoA ligase; HCT: shikimate O -hydroxycinnamoyltransferase; C3′H: coumaroylquinate(coumaroylshikimate)3′-monooxygenase; CCoAOMT: caffeoyl-CoA O -methyltransferase; CCR: cinnamoyl–CoA reductase, CAD: cinnamyl–alcohol dehydrogenase; F5H: ferulate-5-hydroxylase; POD: peroxidase.

Techniques Used: Expressing

26) Product Images from "Comparative Temporal Transcriptome Profiling of Wheat near Isogenic Line Carrying Lr57 under Compatible and Incompatible Interactions"

Article Title: Comparative Temporal Transcriptome Profiling of Wheat near Isogenic Line Carrying Lr57 under Compatible and Incompatible Interactions

Journal: Frontiers in Plant Science

doi: 10.3389/fpls.2016.01943

Hierarchical cluster of 74 differentially expressed NLR genes in WL711 and WL711+Lr57 at different time points . Hierarchical clustering of NLR genes showed peak induction of expression of resistance related genes immediately after infection with the pathogen i.e., at 12 HPI. Genes clusters are on the horizontal axis and samples on veritical axis. Colors on vertical represents the clustered genes based on gene expression, horizontal line represents the single gene and color of the line indicates the average gene expression in specific sample: high expression level in red, low expression level in green.
Figure Legend Snippet: Hierarchical cluster of 74 differentially expressed NLR genes in WL711 and WL711+Lr57 at different time points . Hierarchical clustering of NLR genes showed peak induction of expression of resistance related genes immediately after infection with the pathogen i.e., at 12 HPI. Genes clusters are on the horizontal axis and samples on veritical axis. Colors on vertical represents the clustered genes based on gene expression, horizontal line represents the single gene and color of the line indicates the average gene expression in specific sample: high expression level in red, low expression level in green.

Techniques Used: Expressing, Infection

Co-regulated genes expression network of highly expressed transcription factor with other resistance genes . Hexagon represents the transcription factors with more than 20 connections with nearby genes and circle represents the resistance gene, peroxidases, glucanases, cytochrome P450, ABC transporters, Phenylalanine ammonia lyase, protein kinases and O-methyltransferase. Edges represents the degree of connectivity in depicted by weighted gene matrix. (A) Gene network from cluster 1 of WL711. (B) Gene network from cluster 1 of WL711+ Lr 57.
Figure Legend Snippet: Co-regulated genes expression network of highly expressed transcription factor with other resistance genes . Hexagon represents the transcription factors with more than 20 connections with nearby genes and circle represents the resistance gene, peroxidases, glucanases, cytochrome P450, ABC transporters, Phenylalanine ammonia lyase, protein kinases and O-methyltransferase. Edges represents the degree of connectivity in depicted by weighted gene matrix. (A) Gene network from cluster 1 of WL711. (B) Gene network from cluster 1 of WL711+ Lr 57.

Techniques Used: Expressing

Number of differentially expressed pathways between susceptible and resistant genotypes WL711 and WL711+ Lr57 , respectively .
Figure Legend Snippet: Number of differentially expressed pathways between susceptible and resistant genotypes WL711 and WL711+ Lr57 , respectively .

Techniques Used:

MapMan visualization of defense response in WL711+ Lr 57 after pathogen attack. DEGs (fold changes ≥ 2, p ≤ 0.05) were imported into MapMan . Up- and Down-regulated DEGs are represented with blue and red squares, respectively with log2 transformed values.
Figure Legend Snippet: MapMan visualization of defense response in WL711+ Lr 57 after pathogen attack. DEGs (fold changes ≥ 2, p ≤ 0.05) were imported into MapMan . Up- and Down-regulated DEGs are represented with blue and red squares, respectively with log2 transformed values.

Techniques Used: Transformation Assay

(A) Venn diagram showing overlap of differentially expressed genes between WL711 (blue) and WL711+ Lr57 (yellow) genotypes at different time points; (B) Regulation of differentially expressed genes between WL711 and WL711+ Lr57 .
Figure Legend Snippet: (A) Venn diagram showing overlap of differentially expressed genes between WL711 (blue) and WL711+ Lr57 (yellow) genotypes at different time points; (B) Regulation of differentially expressed genes between WL711 and WL711+ Lr57 .

Techniques Used:

(A) Expression profiling of differentially expressed genes in both WL711 and WL711+ Lr57 . Horizontal row represents the gene and vertical columns denote samples. (B) Venn diagram showing the distribution of differentially expressed genes in WL711 and WL711+ Lr57 . (C) Distribution of differentially expressed genes at different time points post inoculation in WL711. (D) Distribution of differentially expressed genes at different time points post inoculation in WL711+ Lr57 .
Figure Legend Snippet: (A) Expression profiling of differentially expressed genes in both WL711 and WL711+ Lr57 . Horizontal row represents the gene and vertical columns denote samples. (B) Venn diagram showing the distribution of differentially expressed genes in WL711 and WL711+ Lr57 . (C) Distribution of differentially expressed genes at different time points post inoculation in WL711. (D) Distribution of differentially expressed genes at different time points post inoculation in WL711+ Lr57 .

Techniques Used: Expressing

Distribution of differentially expressed transcripts/genes involved in biological processes, molecular functions and cellular components in WL711 and WL711+ Lr57 .
Figure Legend Snippet: Distribution of differentially expressed transcripts/genes involved in biological processes, molecular functions and cellular components in WL711 and WL711+ Lr57 .

Techniques Used:

Differential expression of genes (A) Expression of genes for transcription factors, Pkinase, Pkinase_Tyr, Chitinase, Glucanase, and Pathogenesis-related (PR) proteins. (B) DEG for resistance gene domains for peroxidases, ABC2_membrane (ABC2), Bowman-Birk leg (BB), oxalate oxidase (OO), glutathione s-transferase (GST), caffeic acid 3-o-methyltransferase (CAOM), caffeoyl- o-methyltransferase (COM), and jasmonate o-methyltransferase (JOM) in WL711 and WL711+ Lr57 .
Figure Legend Snippet: Differential expression of genes (A) Expression of genes for transcription factors, Pkinase, Pkinase_Tyr, Chitinase, Glucanase, and Pathogenesis-related (PR) proteins. (B) DEG for resistance gene domains for peroxidases, ABC2_membrane (ABC2), Bowman-Birk leg (BB), oxalate oxidase (OO), glutathione s-transferase (GST), caffeic acid 3-o-methyltransferase (CAOM), caffeoyl- o-methyltransferase (COM), and jasmonate o-methyltransferase (JOM) in WL711 and WL711+ Lr57 .

Techniques Used: Expressing

Experimental set up for studying the differential gene expression in WL711 and WL711+Lr57 after challenge with Puccinia triticina pathotype 77-5 .
Figure Legend Snippet: Experimental set up for studying the differential gene expression in WL711 and WL711+Lr57 after challenge with Puccinia triticina pathotype 77-5 .

Techniques Used: Expressing

27) Product Images from "An Indel Polymorphism in the MtnA 3' Untranslated Region Is Associated with Gene Expression Variation and Local Adaptation in Drosophila melanogaster"

Article Title: An Indel Polymorphism in the MtnA 3' Untranslated Region Is Associated with Gene Expression Variation and Local Adaptation in Drosophila melanogaster

Journal: PLoS Genetics

doi: 10.1371/journal.pgen.1005987

Association between an indel polymorphism in the  MtnA  3' UTR and gene expression variation. (A) An indel (and a linked SNP marked in gray) in the  MtnA  3' UTR are the only polymorphisms within the 6-kb  MtnA  region that show a large difference in frequency between an African and a European population of  D .  melanogaster . A comparison with three outgroup species,  D .  sechellia  (Sec),  D .  simulans  (Sim) and  D .  yakuba  (Yak), indicated that the deletion is the derived variant. (B)  MtnA  expression in the brain and the gut of eight European (NL) lines, shown in blue, and eight African (ZK) lines, shown in green. The two European lines lacking the deletion,  NL11  and  NL15 , show lower  MtnA  expression than those with the deletion.
Figure Legend Snippet: Association between an indel polymorphism in the MtnA 3' UTR and gene expression variation. (A) An indel (and a linked SNP marked in gray) in the MtnA 3' UTR are the only polymorphisms within the 6-kb MtnA region that show a large difference in frequency between an African and a European population of D . melanogaster . A comparison with three outgroup species, D . sechellia (Sec), D . simulans (Sim) and D . yakuba (Yak), indicated that the deletion is the derived variant. (B) MtnA expression in the brain and the gut of eight European (NL) lines, shown in blue, and eight African (ZK) lines, shown in green. The two European lines lacking the deletion, NL11 and NL15 , show lower MtnA expression than those with the deletion.

Techniques Used: Expressing, Size-exclusion Chromatography, Derivative Assay, Variant Assay

Evidence for positive selection at the  MtnA  locus. (A) Watterson’s  θ  of  D .  melanogaster  populations from Zimbabwe (ZK), the Netherlands (NL) and Sweden (SU) calculated in sliding windows of 500 bp with a step size of 250 bp. (B)  F st  values for pairwise comparisons of ZK, NL and SU calculated in sliding windows of 500 bp with a step size of 250 bp. (C) Selective sweep  (SweepFinder)  analysis of the Netherlands population showing the composite likelihood ratio (CLR) statistic in sliding windows of 1000 bp. (D) Selective sweep ( SweepFinder ) analysis of the Swedish population showing the CLR statistic in sliding windows of 1000 bp. The black line indicates the 5% significance threshold calculated using the demographic model of Duchen et al. [  5 ] for neutral simulations. The red line indicates the 5% significance threshold calculated using the demographic model of Werzner et al. [  6 ] for neutral simulations and the gray dashed line indicates the 5% significance threshold using the model of Thornton and Andolfatto [  35 ]. (E) Gene models for the 6-kb region analyzed. The gray highlighted region indicates the position of the 49-bp indel polymorphism in the  MtnA  3’ UTR.
Figure Legend Snippet: Evidence for positive selection at the MtnA locus. (A) Watterson’s θ of D . melanogaster populations from Zimbabwe (ZK), the Netherlands (NL) and Sweden (SU) calculated in sliding windows of 500 bp with a step size of 250 bp. (B) F st values for pairwise comparisons of ZK, NL and SU calculated in sliding windows of 500 bp with a step size of 250 bp. (C) Selective sweep (SweepFinder) analysis of the Netherlands population showing the composite likelihood ratio (CLR) statistic in sliding windows of 1000 bp. (D) Selective sweep ( SweepFinder ) analysis of the Swedish population showing the CLR statistic in sliding windows of 1000 bp. The black line indicates the 5% significance threshold calculated using the demographic model of Duchen et al. [ 5 ] for neutral simulations. The red line indicates the 5% significance threshold calculated using the demographic model of Werzner et al. [ 6 ] for neutral simulations and the gray dashed line indicates the 5% significance threshold using the model of Thornton and Andolfatto [ 35 ]. (E) Gene models for the 6-kb region analyzed. The gray highlighted region indicates the position of the 49-bp indel polymorphism in the MtnA 3’ UTR.

Techniques Used: Selection

Reporter gene constructs and their expression. (A) The gray boxes represent the  MtnA  promoter, which is identical between the African and European alleles. The white boxes represent the GFP/ lacZ  reporter genes. The blue hatched box represents the  MtnA  3’ UTR with the deletion. The green box represents the  MtnA 3’  UTR with the additional 49 bp marked in red. The same color scheme applies to the bar plots. (B) The two versions of the GFP reporter gene differ significantly in expression in heads ( t -test,  P  = 0.0019) and bodies ( t -test,  P  = 0.0046), as assayed by qRT-PCR. (C) The two versions of the  lacZ  reporter gene differed significantly in expression in heads ( t -test,  P  = 0.0006) and guts ( t -test,  P =  0.0001) as measured by β-galactosidase enzymatic activity. The error bars represent the standard error of the mean.
Figure Legend Snippet: Reporter gene constructs and their expression. (A) The gray boxes represent the MtnA promoter, which is identical between the African and European alleles. The white boxes represent the GFP/ lacZ reporter genes. The blue hatched box represents the MtnA 3’ UTR with the deletion. The green box represents the MtnA 3’ UTR with the additional 49 bp marked in red. The same color scheme applies to the bar plots. (B) The two versions of the GFP reporter gene differ significantly in expression in heads ( t -test, P = 0.0019) and bodies ( t -test, P = 0.0046), as assayed by qRT-PCR. (C) The two versions of the lacZ reporter gene differed significantly in expression in heads ( t -test, P = 0.0006) and guts ( t -test, P = 0.0001) as measured by β-galactosidase enzymatic activity. The error bars represent the standard error of the mean.

Techniques Used: Construct, Expressing, Quantitative RT-PCR, Activity Assay

Proportional mortality after oxidative stress. (A) RNAi-mediated  MtnA  knockdown (hatched lines) and control flies (solid lines).  P -values are shown for within population/background comparisons. (B) Dutch (blue) and Malaysian (orange) flies with the deletion (hatched lines) and without the deletion (solid lines) in the  MtnA  3’ UTR. Error bars indicate the standard error of the mean. * P
Figure Legend Snippet: Proportional mortality after oxidative stress. (A) RNAi-mediated MtnA knockdown (hatched lines) and control flies (solid lines). P -values are shown for within population/background comparisons. (B) Dutch (blue) and Malaysian (orange) flies with the deletion (hatched lines) and without the deletion (solid lines) in the MtnA 3’ UTR. Error bars indicate the standard error of the mean. * P

Techniques Used:

Expression of an  MtnA -GFP reporter gene in the brain. (A-C) GFP expression driven by the reporter gene construct with the ancestral  MtnA  3’ UTR variant. (D-G) Higher magnification of the brain regions where GFP is expressed. AL: antennal lobe, MB: mushroom bodies, SOG: subesophageal ganglion, Lo: lobula, Me: medulla. In (G) the arrow indicates cells expressing GFP. Green: GFP, red: anti-disclarge, targeting general neuropil.
Figure Legend Snippet: Expression of an MtnA -GFP reporter gene in the brain. (A-C) GFP expression driven by the reporter gene construct with the ancestral MtnA 3’ UTR variant. (D-G) Higher magnification of the brain regions where GFP is expressed. AL: antennal lobe, MB: mushroom bodies, SOG: subesophageal ganglion, Lo: lobula, Me: medulla. In (G) the arrow indicates cells expressing GFP. Green: GFP, red: anti-disclarge, targeting general neuropil.

Techniques Used: Expressing, Construct, Variant Assay

28) Product Images from "Small RNA bidirectional crosstalk during the interaction between wheat and Zymoseptoria tritici"

Article Title: Small RNA bidirectional crosstalk during the interaction between wheat and Zymoseptoria tritici

Journal: bioRxiv

doi: 10.1101/501593

Wheat induces sRNAs to regulate wheat genes as an immune response against Z. tritici . (A) The functions of the wheat genes, which were downregulated and predicted to be targeted by wheat induced sRNAs. (B,C,D,E) Degradome analysis of the wheat genes targeted by miRNA-uniq-133, miRNA-uniq-113 and siRNA180.
Figure Legend Snippet: Wheat induces sRNAs to regulate wheat genes as an immune response against Z. tritici . (A) The functions of the wheat genes, which were downregulated and predicted to be targeted by wheat induced sRNAs. (B,C,D,E) Degradome analysis of the wheat genes targeted by miRNA-uniq-133, miRNA-uniq-113 and siRNA180.

Techniques Used:

29) Product Images from "Mutation in sorghum LOW GERMINATION STIMULANT 1 alters strigolactones and causes Striga resistance"

Article Title: Mutation in sorghum LOW GERMINATION STIMULANT 1 alters strigolactones and causes Striga resistance

Journal: Proceedings of the National Academy of Sciences of the United States of America

doi: 10.1073/pnas.1618965114

Sequence comparison of WT Shanqui Red ( LGS1 ) and mutant alleles from Tetron ( lgs1-5 ) and SC103 ( lgs1-4 ) with the sorghum reference genome, BTx623 for the reverse strand of Sobic.005G213600 . Genomic sequences of Shanqui Red and the mutants are from consensus
Figure Legend Snippet: Sequence comparison of WT Shanqui Red ( LGS1 ) and mutant alleles from Tetron ( lgs1-5 ) and SC103 ( lgs1-4 ) with the sorghum reference genome, BTx623 for the reverse strand of Sobic.005G213600 . Genomic sequences of Shanqui Red and the mutants are from consensus

Techniques Used: Sequencing, Mutagenesis, Genomic Sequencing

Chemical phenotypes of LGS1 variants. SL profiles of root exudates from sorghum Shanqui Red ( LGS1 ) with high Striga germination stimulant activity, and of five low-stimulant lines with mutant alleles at SRN39 ( lgs1-1 ), 555 ( lgs1-2 ), IS7777 ( lgs1-3 ), SC103
Figure Legend Snippet: Chemical phenotypes of LGS1 variants. SL profiles of root exudates from sorghum Shanqui Red ( LGS1 ) with high Striga germination stimulant activity, and of five low-stimulant lines with mutant alleles at SRN39 ( lgs1-1 ), 555 ( lgs1-2 ), IS7777 ( lgs1-3 ), SC103

Techniques Used: Activity Assay, Mutagenesis

30) Product Images from "Transcriptomic analysis of the differentiating ovary of the protogynous ricefield eel Monopterus albus"

Article Title: Transcriptomic analysis of the differentiating ovary of the protogynous ricefield eel Monopterus albus

Journal: BMC Genomics

doi: 10.1186/s12864-017-3953-6

Expression of functional genes of the retinol metabolism pathway in gonads of ricefield eel larvae at 6, 9, 12, and 20 dph. Y-axis shows FPKM values of genes inferred from the transcriptome data. The asterisk-marked genes were further analyzed and confirmed by qPCR. HS6: 6 dph; HS9: 9 dph; HS12: 12 dph; HS20: 20 dph
Figure Legend Snippet: Expression of functional genes of the retinol metabolism pathway in gonads of ricefield eel larvae at 6, 9, 12, and 20 dph. Y-axis shows FPKM values of genes inferred from the transcriptome data. The asterisk-marked genes were further analyzed and confirmed by qPCR. HS6: 6 dph; HS9: 9 dph; HS12: 12 dph; HS20: 20 dph

Techniques Used: Expressing, Functional Assay, Real-time Polymerase Chain Reaction

Differential expression of some representative genes during gonadal development of ricefield eel larvae. Y-axis shows the fold changes in mRNA expression of genes in the designated comparison. HS6: 6 dph; HS9: 9 dph; HS12: 12 dph; HS20: 20 dph. The columns above and below X-axis indicate up-regulation and down-regulation, respectively
Figure Legend Snippet: Differential expression of some representative genes during gonadal development of ricefield eel larvae. Y-axis shows the fold changes in mRNA expression of genes in the designated comparison. HS6: 6 dph; HS9: 9 dph; HS12: 12 dph; HS20: 20 dph. The columns above and below X-axis indicate up-regulation and down-regulation, respectively

Techniques Used: Expressing

The gonadal histology of ricefield eel larvae. a The gonad at 6 dph. The primordial germ cell (PGC) was in isolated states. b The gonad at 9 dph. The ovarian cavities could be observed. c The gonad at 12 dph. The number of PGCs increased greatly and the majority of germ cells showed clear borders and most likely developed as oogonia. d The gonad at 20 dph. The cytoplasm of oogonium was inconspicuous, and the borders of nuclei were very clear. Some germ cells () containing condensate chromatins might have developed into pachytene oocytes. The inset is the magnification of the boxed area in each image (Scale bar = 5 μm). PGC, Primordial germ cell; BV, blood vessel; IN, intestine; YS, yolk sac; MD, mesonephric duct; KI, kidney; ME, mesentery; GW, gonadal wall; MO, mesogonium; NU, nucleolus; OC, ovarian cavity; Oog, oogonium; Oo, oocytes; dph, days post hatching; Scale bar = 25 μm except the insets
Figure Legend Snippet: The gonadal histology of ricefield eel larvae. a The gonad at 6 dph. The primordial germ cell (PGC) was in isolated states. b The gonad at 9 dph. The ovarian cavities could be observed. c The gonad at 12 dph. The number of PGCs increased greatly and the majority of germ cells showed clear borders and most likely developed as oogonia. d The gonad at 20 dph. The cytoplasm of oogonium was inconspicuous, and the borders of nuclei were very clear. Some germ cells () containing condensate chromatins might have developed into pachytene oocytes. The inset is the magnification of the boxed area in each image (Scale bar = 5 μm). PGC, Primordial germ cell; BV, blood vessel; IN, intestine; YS, yolk sac; MD, mesonephric duct; KI, kidney; ME, mesentery; GW, gonadal wall; MO, mesogonium; NU, nucleolus; OC, ovarian cavity; Oog, oogonium; Oo, oocytes; dph, days post hatching; Scale bar = 25 μm except the insets

Techniques Used: Pyrolysis Gas Chromatography, Isolation

Homology analysis of the gonadal transcriptome of ricefield eel larvae. All distinct gene sequences that had BLAST annotations within the Nr database with a cutoff e-value ≤ 10 −5 were analyzed for e-value distribution a , similarity distribution b , and species distribution c
Figure Legend Snippet: Homology analysis of the gonadal transcriptome of ricefield eel larvae. All distinct gene sequences that had BLAST annotations within the Nr database with a cutoff e-value ≤ 10 −5 were analyzed for e-value distribution a , similarity distribution b , and species distribution c

Techniques Used:

Expression of early gonadal development-related functional genes in gonads of ricefield eel larvae at 6, 9, 12, and 20 dph. Y-axis shows FPKM values of genes inferred from the transcriptome data. The asterisk-marked genes were further analyzed and confirmed by qPCR. HS6: 6 dph; HS9: 9 dph; HS12: 12 dph; HS20: 20 dph
Figure Legend Snippet: Expression of early gonadal development-related functional genes in gonads of ricefield eel larvae at 6, 9, 12, and 20 dph. Y-axis shows FPKM values of genes inferred from the transcriptome data. The asterisk-marked genes were further analyzed and confirmed by qPCR. HS6: 6 dph; HS9: 9 dph; HS12: 12 dph; HS20: 20 dph

Techniques Used: Expressing, Functional Assay, Real-time Polymerase Chain Reaction

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Article Title: Oxidative Stress Is a Mediator for Increased Lipid Accumulation in a Newly Isolated Dunaliella salina Strain
Article Snippet: .. The partial sequence of the 18S rDNA encoding gene was submitted to National Center for Biotechnology Information (NCBI) GeneBank database as Dunaliella salina strain Tuz_KS_01 (GeneBank accession no. JX880083 ). .. According to Basic Local Aligment Search Tool (BLAST) analysis, the isolated sequence had very high percentage of identity with other deposited 18S rDNA sequences of Dunaliella species shown in the phylogenetic tree plotted in .

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Article Title: Human giant congenital melanocytic nevus exhibits potential proteomic alterations leading to melanotumorigenesis
Article Snippet: Bioinformatics analysis A systemic bioinformatics analysis of the GCMN proteome was conducted using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING 8.3) [ ], the Protein Analysis Through Evolutionary Relationships classification system (PANTHER 7.0) [ ], the National Center for Biotechnology Information (NCBI) COG database [ ], Cytoscape, and ClueGO [ ].

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