Journal: bioRxiv

Article Title: The Drosophila TART transposon manipulates the piRNA pathway as a counter-defense strategy to limit host silencing

doi: 10.1101/2020.02.20.957324

Figure Lengend Snippet: (A) GBrowse screenshot from FlyBase showing the nxf2 gene model along with the annotated TART-A TE insertion. Note that the TART-A annotation overlaps the 3’ coding sequence of nxf2 . (B) BLAST hits between the RepBase TART-A sequence and the nxf2 transcript. Each colored box represents a single BLAST alignment. The 5’ UTR of TART-A is copied from its 3’ UTR during replication. The two UTRs are therefore identical in sequence and the homology between nxf2 and the TART-A 3’ UTR is mirrored in the 5’ UTR. (C). A zoomed-out multiple sequence alignment of nxf2 orthologs for six species from the melanogaster species group shows that the TART-like region of nxf2 is present in all six species.

Article Snippet: We used Illumina genomic sequencing data from the DGRP ( ; ) to estimate TART-A copy number.

Techniques: Sequencing

Journal: bioRxiv

Article Title: The Drosophila TART transposon manipulates the piRNA pathway as a counter-defense strategy to limit host silencing

doi: 10.1101/2020.02.20.957324

Figure Lengend Snippet: We used NCBI web BLAST to search the D. melanogaster Nxf2 peptide sequence against the RefSeq peptide database and identified homologs in 22 Drosophila species. The C-terminal region of Nxf2 derives from coding sequence which shares homology with the TART-A transposable element (grey box). At the peptide level, this region is conserved out to D. virilis , which suggests that, if it was acquired from an insertion of the TART-A TE, the insertion would have occurred in the common ancestor of the entire genus.

Article Snippet: We used Illumina genomic sequencing data from the DGRP ( ; ) to estimate TART-A copy number.

Techniques: Sequencing

Journal: bioRxiv

Article Title: The Drosophila TART transposon manipulates the piRNA pathway as a counter-defense strategy to limit host silencing

doi: 10.1101/2020.02.20.957324

Figure Lengend Snippet: (A) Dotplot comparing D. melanogaster TART-A to its homologs in D. yakuba and D. sechellia . The diagonal lines denote regions of homology while the pink boxes show the location of the nxf2 -like sequence in the D. melanogaster TART-A . Neither the D. yakuba nor the D. sechellia TART-A sequences contain nxf2 -like sequence. However, the regions directly flanking the nxf2 -like sequence in D. melanogaster are also present in D. yakuba (see Figure S2 for magnified view). (B) Gene tree showing relative age of shared homology. We aligned the nxf2 -like sequences from nine copies of TART-A in the D. melanogaster reference genome to the nxf2 transcripts from six Drosophila species and inferred a maximum likelihood phylogeny using RAxML. D. melanogaster nxf2 is most closely related to the nxf2 -like sequences present in the D. melanogaster TART-A copies, suggesting the shared homology occurred after the divergence between D. melanogaster and D. simulans .

Article Snippet: We used Illumina genomic sequencing data from the DGRP ( ; ) to estimate TART-A copy number.

Techniques: Sequencing

Journal: bioRxiv

Article Title: The Drosophila TART transposon manipulates the piRNA pathway as a counter-defense strategy to limit host silencing

doi: 10.1101/2020.02.20.957324

Figure Lengend Snippet: (A) We aligned previously published piRNA data from the D. melanogaster Drosophila Genetic Reference Panel (DGRP) to TART-A and examined read coverage across the element. We find abundant sense and antisense piRNA production across most of the element, including the regions containing the nxf2 -like sequence (grey boxes). Note that the 5’ UTR of TART-A is copied from the 3’ UTR during replication and is therefore identical in sequence. We masked the 5’ UTR (positions 1-4000) for this analysis. (B) The length of aligned reads are consistent with that expected for piRNAs and the TART-A derived piRNAs are biased towards the minus strand. (C) TART-A piRNAs show an enrichment of alignments where the 5’ end of one piRNA is found directly after the 3’ end of the previous piRNA (i.e. distance of 1), consistent with piRNA phasing. (D) Unlike TART-A, nxf2 produces piRNAs primarily in the regions directly downstream from its TART -like sequence (grey boxes). The vast majority of these piRNAs are only from the sense strand of nxf2 (panel E) and also show the signature of phasing (panel F). Note that the TART -like sequence of nxf2 was masked for this analysis to avoid cross-mapping of TART -derived piRNAs to the nxf2 transcript.

Article Snippet: We used Illumina genomic sequencing data from the DGRP ( ; ) to estimate TART-A copy number.

Techniques: Sequencing, Derivative Assay

Journal: bioRxiv

Article Title: The Drosophila TART transposon manipulates the piRNA pathway as a counter-defense strategy to limit host silencing

doi: 10.1101/2020.02.20.957324

Figure Lengend Snippet: We inferred TART-A copy-number for 151 DGRP strains using published Illumina sequencing data ( ; ) and retrieved expression values for nxf2 from microarray data from whole adult females . We found that TART-A copy number is significantly negatively correlated with nxf2 expression levels, as expected if TART-A piRNAs are targeting nxf2 for suppression (Spearman’s rho = -0.48, P = 4.6e-10).

Article Snippet: We used Illumina genomic sequencing data from the DGRP ( ; ) to estimate TART-A copy number.

Techniques: Illumina Sequencing, Expressing, Microarray

Journal: Cell Reports

Article Title: Highly mutated antibodies capable of neutralizing N276 glycan-deficient HIV after a single immunization with an Env trimer

doi: 10.1016/j.celrep.2022.110485

Figure Lengend Snippet:

Article Snippet: 10X Genomics BCR sequencing FASTQ data are submitted under BioProject: PRJNA802246.

Techniques: Purification, Blocking Assay, Virus, Glycoproteomics, Mutagenesis, Recombinant, Produced, Adjuvant, Enzyme-linked Immunosorbent Assay, Transfection, Staining, Luciferase, Cell Isolation, Labeling, Multiplex Assay, Reverse Transcription, Expressing, Sequencing, Software, Binding Assay

Journal: Data in Brief

Article Title: Whole genome sequence data of Streptomyces californicus TBG-201, a chitinolytic actinomycete isolated from the Vandanam sacred groves of Alleppey District, Kerala, India

doi: 10.1016/j.dib.2023.109228

Figure Lengend Snippet: The general characteristics of the S. californicus TBG-201 genome.

Article Snippet: Whole genome sequence data of a chitinolytic actinomycete, Streptomyces californicus TBG-201 (Original data) (Mendeley Data).

Techniques: Sequencing, CRISPR

Journal: Data in Brief

Article Title: Whole genome sequence data of Streptomyces californicus TBG-201, a chitinolytic actinomycete isolated from the Vandanam sacred groves of Alleppey District, Kerala, India

doi: 10.1016/j.dib.2023.109228

Figure Lengend Snippet: Genes for chitin degradation identified from S. californicus TBG-201 genome.

Article Snippet: Whole genome sequence data of a chitinolytic actinomycete, Streptomyces californicus TBG-201 (Original data) (Mendeley Data).

Techniques: Histone Deacetylase Assay

Journal: Data in Brief

Article Title: Whole genome sequence data of Streptomyces californicus TBG-201, a chitinolytic actinomycete isolated from the Vandanam sacred groves of Alleppey District, Kerala, India

doi: 10.1016/j.dib.2023.109228

Figure Lengend Snippet: Secondary metabolite clusters of S. californicus TBG-201 as determined by antiSMASH.

Article Snippet: Whole genome sequence data of a chitinolytic actinomycete, Streptomyces californicus TBG-201 (Original data) (Mendeley Data).

Techniques:

Journal: Scientific Data

Article Title: Chromosome-level genome assembly and annotation of the prickly nightshade Solanum rostratum Dunal

doi: 10.1038/s41597-023-02247-3

Figure Lengend Snippet: Statistics of sequencing data for Solanum rostratum genome assembly and annotation.

Article Snippet: All raw sequencing data have been deposited in the NCBI Sequence Read Archive (SRA) (Table ) under Bioproject number PRJNA932047, including the genomic Illumina sequencing data (SRR23354532) , genomic PacBio HiFi sequencing data (SRR23354533) , transcriptome Illumina sequencing data (SRR23354526-SRR23354530) – , Hi-C sequencing data (SRR23354531) , and transcriptome Pacbio-Sequel II sequencing data (SRR23354525) .

Techniques: Sequencing