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  • 92
    Millipore coffea arabica
    Coffea Arabica, supplied by Millipore, used in various techniques. Bioz Stars score: 92/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Lomapharm coffea arabica l
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    Applied Genetics Laboratories coffee coffea arabica l theoretical
    Coffee Coffea Arabica L Theoretical, supplied by Applied Genetics Laboratories, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Medicago coffea canephora
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    Biotechnology Information coffea canephora
    Analysis of the evolutionary history of the ECH genes in the syntenic regions in different <t>Solanaceae</t> species. ( A ) Phylogenetic tree of ECH genes homologous to Sl-AECH1 . Genes colored with orange and labeled with orange rectangles are from the syntenic regions of Solanaceae species shown in panel ( B ). Genes marked with stars have been tested involved in acylsugar biosynthesis. ( B ) The acylsugar gene cluster syntenic regions of 11 Solanaceae species and two outgroup species Ipomea trifida (Convolvulaceae) and <t>Coffea</t> canephora (Rubiaceae). ( C ) Reconciled evolutionary history of ECH enzyme based on panel ( A ) and ( B ). The colors of the branches correspond to different lineages shown in panel A. Grey branch means enzymes from that lineage could not be found through BLAST and may have been lost. Numbers in the circle indicate the nodes in the phylogenetic tree as shown in panel ( A ). The inferred evolutionary events were shown next to the nodes. Grey box highlighted the evolutionary history of the genes in the syntenic regions. Before the Solanaceae specific WGD events, an ECH was inserted into the syntenic region through unknown mechanism. After the WGD events, there was one ECH gene in each syntenic region on Chr07 and Chr12. Before the divergence of Solanum , Nicotiana , and Petunia species, the ECH gene on Chr07 had experienced a tandem duplication event, leading to two branches on the phylogenetic tree. During the speciation, the ECH gene on Chr12 was deleted from the genome in the most recent common ancestor of Nicotiana and Solanum after divergent from Petunia , while one of the tandem duplicates on Chr07 was lost in Petunia .
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    91
    Takeda coffea canephora
    Analysis of the evolutionary history of the ECH genes in the syntenic regions in different <t>Solanaceae</t> species. ( A ) Phylogenetic tree of ECH genes homologous to Sl-AECH1 . Genes colored with orange and labeled with orange rectangles are from the syntenic regions of Solanaceae species shown in panel ( B ). Genes marked with stars have been tested involved in acylsugar biosynthesis. ( B ) The acylsugar gene cluster syntenic regions of 11 Solanaceae species and two outgroup species Ipomea trifida (Convolvulaceae) and <t>Coffea</t> canephora (Rubiaceae). ( C ) Reconciled evolutionary history of ECH enzyme based on panel ( A ) and ( B ). The colors of the branches correspond to different lineages shown in panel A. Grey branch means enzymes from that lineage could not be found through BLAST and may have been lost. Numbers in the circle indicate the nodes in the phylogenetic tree as shown in panel ( A ). The inferred evolutionary events were shown next to the nodes. Grey box highlighted the evolutionary history of the genes in the syntenic regions. Before the Solanaceae specific WGD events, an ECH was inserted into the syntenic region through unknown mechanism. After the WGD events, there was one ECH gene in each syntenic region on Chr07 and Chr12. Before the divergence of Solanum , Nicotiana , and Petunia species, the ECH gene on Chr07 had experienced a tandem duplication event, leading to two branches on the phylogenetic tree. During the speciation, the ECH gene on Chr12 was deleted from the genome in the most recent common ancestor of Nicotiana and Solanum after divergent from Petunia , while one of the tandem duplicates on Chr07 was lost in Petunia .
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    Applied Genetics Laboratories coffea liberica var
    Analysis of the evolutionary history of the ECH genes in the syntenic regions in different <t>Solanaceae</t> species. ( A ) Phylogenetic tree of ECH genes homologous to Sl-AECH1 . Genes colored with orange and labeled with orange rectangles are from the syntenic regions of Solanaceae species shown in panel ( B ). Genes marked with stars have been tested involved in acylsugar biosynthesis. ( B ) The acylsugar gene cluster syntenic regions of 11 Solanaceae species and two outgroup species Ipomea trifida (Convolvulaceae) and <t>Coffea</t> canephora (Rubiaceae). ( C ) Reconciled evolutionary history of ECH enzyme based on panel ( A ) and ( B ). The colors of the branches correspond to different lineages shown in panel A. Grey branch means enzymes from that lineage could not be found through BLAST and may have been lost. Numbers in the circle indicate the nodes in the phylogenetic tree as shown in panel ( A ). The inferred evolutionary events were shown next to the nodes. Grey box highlighted the evolutionary history of the genes in the syntenic regions. Before the Solanaceae specific WGD events, an ECH was inserted into the syntenic region through unknown mechanism. After the WGD events, there was one ECH gene in each syntenic region on Chr07 and Chr12. Before the divergence of Solanum , Nicotiana , and Petunia species, the ECH gene on Chr07 had experienced a tandem duplication event, leading to two branches on the phylogenetic tree. During the speciation, the ECH gene on Chr12 was deleted from the genome in the most recent common ancestor of Nicotiana and Solanum after divergent from Petunia , while one of the tandem duplicates on Chr07 was lost in Petunia .
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    Applied Genetics Laboratories genus coffea l theoretical
    Analysis of the evolutionary history of the ECH genes in the syntenic regions in different <t>Solanaceae</t> species. ( A ) Phylogenetic tree of ECH genes homologous to Sl-AECH1 . Genes colored with orange and labeled with orange rectangles are from the syntenic regions of Solanaceae species shown in panel ( B ). Genes marked with stars have been tested involved in acylsugar biosynthesis. ( B ) The acylsugar gene cluster syntenic regions of 11 Solanaceae species and two outgroup species Ipomea trifida (Convolvulaceae) and <t>Coffea</t> canephora (Rubiaceae). ( C ) Reconciled evolutionary history of ECH enzyme based on panel ( A ) and ( B ). The colors of the branches correspond to different lineages shown in panel A. Grey branch means enzymes from that lineage could not be found through BLAST and may have been lost. Numbers in the circle indicate the nodes in the phylogenetic tree as shown in panel ( A ). The inferred evolutionary events were shown next to the nodes. Grey box highlighted the evolutionary history of the genes in the syntenic regions. Before the Solanaceae specific WGD events, an ECH was inserted into the syntenic region through unknown mechanism. After the WGD events, there was one ECH gene in each syntenic region on Chr07 and Chr12. Before the divergence of Solanum , Nicotiana , and Petunia species, the ECH gene on Chr07 had experienced a tandem duplication event, leading to two branches on the phylogenetic tree. During the speciation, the ECH gene on Chr12 was deleted from the genome in the most recent common ancestor of Nicotiana and Solanum after divergent from Petunia , while one of the tandem duplicates on Chr07 was lost in Petunia .
    Genus Coffea L Theoretical, supplied by Applied Genetics Laboratories, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Unigene coffea canephora unigene
    Analysis of the evolutionary history of the ECH genes in the syntenic regions in different <t>Solanaceae</t> species. ( A ) Phylogenetic tree of ECH genes homologous to Sl-AECH1 . Genes colored with orange and labeled with orange rectangles are from the syntenic regions of Solanaceae species shown in panel ( B ). Genes marked with stars have been tested involved in acylsugar biosynthesis. ( B ) The acylsugar gene cluster syntenic regions of 11 Solanaceae species and two outgroup species Ipomea trifida (Convolvulaceae) and <t>Coffea</t> canephora (Rubiaceae). ( C ) Reconciled evolutionary history of ECH enzyme based on panel ( A ) and ( B ). The colors of the branches correspond to different lineages shown in panel A. Grey branch means enzymes from that lineage could not be found through BLAST and may have been lost. Numbers in the circle indicate the nodes in the phylogenetic tree as shown in panel ( A ). The inferred evolutionary events were shown next to the nodes. Grey box highlighted the evolutionary history of the genes in the syntenic regions. Before the Solanaceae specific WGD events, an ECH was inserted into the syntenic region through unknown mechanism. After the WGD events, there was one ECH gene in each syntenic region on Chr07 and Chr12. Before the divergence of Solanum , Nicotiana , and Petunia species, the ECH gene on Chr07 had experienced a tandem duplication event, leading to two branches on the phylogenetic tree. During the speciation, the ECH gene on Chr12 was deleted from the genome in the most recent common ancestor of Nicotiana and Solanum after divergent from Petunia , while one of the tandem duplicates on Chr07 was lost in Petunia .
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    Applied Genetics Laboratories coffea interspecific backcross progency
    Analysis of the evolutionary history of the ECH genes in the syntenic regions in different <t>Solanaceae</t> species. ( A ) Phylogenetic tree of ECH genes homologous to Sl-AECH1 . Genes colored with orange and labeled with orange rectangles are from the syntenic regions of Solanaceae species shown in panel ( B ). Genes marked with stars have been tested involved in acylsugar biosynthesis. ( B ) The acylsugar gene cluster syntenic regions of 11 Solanaceae species and two outgroup species Ipomea trifida (Convolvulaceae) and <t>Coffea</t> canephora (Rubiaceae). ( C ) Reconciled evolutionary history of ECH enzyme based on panel ( A ) and ( B ). The colors of the branches correspond to different lineages shown in panel A. Grey branch means enzymes from that lineage could not be found through BLAST and may have been lost. Numbers in the circle indicate the nodes in the phylogenetic tree as shown in panel ( A ). The inferred evolutionary events were shown next to the nodes. Grey box highlighted the evolutionary history of the genes in the syntenic regions. Before the Solanaceae specific WGD events, an ECH was inserted into the syntenic region through unknown mechanism. After the WGD events, there was one ECH gene in each syntenic region on Chr07 and Chr12. Before the divergence of Solanum , Nicotiana , and Petunia species, the ECH gene on Chr07 had experienced a tandem duplication event, leading to two branches on the phylogenetic tree. During the speciation, the ECH gene on Chr12 was deleted from the genome in the most recent common ancestor of Nicotiana and Solanum after divergent from Petunia , while one of the tandem duplicates on Chr07 was lost in Petunia .
    Coffea Interspecific Backcross Progency, supplied by Applied Genetics Laboratories, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Lallemand coffea coffee hydroxycinnamoyl coa
    Analysis of the evolutionary history of the ECH genes in the syntenic regions in different <t>Solanaceae</t> species. ( A ) Phylogenetic tree of ECH genes homologous to Sl-AECH1 . Genes colored with orange and labeled with orange rectangles are from the syntenic regions of Solanaceae species shown in panel ( B ). Genes marked with stars have been tested involved in acylsugar biosynthesis. ( B ) The acylsugar gene cluster syntenic regions of 11 Solanaceae species and two outgroup species Ipomea trifida (Convolvulaceae) and <t>Coffea</t> canephora (Rubiaceae). ( C ) Reconciled evolutionary history of ECH enzyme based on panel ( A ) and ( B ). The colors of the branches correspond to different lineages shown in panel A. Grey branch means enzymes from that lineage could not be found through BLAST and may have been lost. Numbers in the circle indicate the nodes in the phylogenetic tree as shown in panel ( A ). The inferred evolutionary events were shown next to the nodes. Grey box highlighted the evolutionary history of the genes in the syntenic regions. Before the Solanaceae specific WGD events, an ECH was inserted into the syntenic region through unknown mechanism. After the WGD events, there was one ECH gene in each syntenic region on Chr07 and Chr12. Before the divergence of Solanum , Nicotiana , and Petunia species, the ECH gene on Chr07 had experienced a tandem duplication event, leading to two branches on the phylogenetic tree. During the speciation, the ECH gene on Chr12 was deleted from the genome in the most recent common ancestor of Nicotiana and Solanum after divergent from Petunia , while one of the tandem duplicates on Chr07 was lost in Petunia .
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    Illumina Inc coffeae
    Quantitative RT-PCR validation of DGE analysis. Relative quantification was carried out to measure changes of selective WRKY gene expression in P . <t>coffeae</t> resistant and susceptible root sample relative to an endogenous reference gene (RPS2). Red line shows the expression analysis in DGE. Data (technical triplicates of three biological experiments) are reported as means ± standard error.
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    Illumina Inc p coffeae
    Time-course expression profiles of 8 defence-related genes in ramie roots during incompatible (●) and compatible (Δ) interactions with P. <t>coffeae</t> revealed by qRT-PCR analyses. ( a ) TI , Trypsin inhibitor; ( b ) PI , Proteinase inhibitor; ( c ) CPI , Cysteine protease inhibitor; ( d ) SOD , Superoxide dismutase; ( e ) PPO , Polyphenoloxidase; ( f ) CHI , Chitinase; ( g ) ERF , Ethylene-responsive transcription factor; and ( h ) LOX , Lipoxygenase. Data from qRT-PCR are means of three biological replicates (each has 2 experimental replicates) and bars represent standerd error.
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    Image Search Results


    Analysis of the evolutionary history of the ECH genes in the syntenic regions in different Solanaceae species. ( A ) Phylogenetic tree of ECH genes homologous to Sl-AECH1 . Genes colored with orange and labeled with orange rectangles are from the syntenic regions of Solanaceae species shown in panel ( B ). Genes marked with stars have been tested involved in acylsugar biosynthesis. ( B ) The acylsugar gene cluster syntenic regions of 11 Solanaceae species and two outgroup species Ipomea trifida (Convolvulaceae) and Coffea canephora (Rubiaceae). ( C ) Reconciled evolutionary history of ECH enzyme based on panel ( A ) and ( B ). The colors of the branches correspond to different lineages shown in panel A. Grey branch means enzymes from that lineage could not be found through BLAST and may have been lost. Numbers in the circle indicate the nodes in the phylogenetic tree as shown in panel ( A ). The inferred evolutionary events were shown next to the nodes. Grey box highlighted the evolutionary history of the genes in the syntenic regions. Before the Solanaceae specific WGD events, an ECH was inserted into the syntenic region through unknown mechanism. After the WGD events, there was one ECH gene in each syntenic region on Chr07 and Chr12. Before the divergence of Solanum , Nicotiana , and Petunia species, the ECH gene on Chr07 had experienced a tandem duplication event, leading to two branches on the phylogenetic tree. During the speciation, the ECH gene on Chr12 was deleted from the genome in the most recent common ancestor of Nicotiana and Solanum after divergent from Petunia , while one of the tandem duplicates on Chr07 was lost in Petunia .

    Journal: eLife

    Article Title: Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity

    doi: 10.7554/eLife.56717

    Figure Lengend Snippet: Analysis of the evolutionary history of the ECH genes in the syntenic regions in different Solanaceae species. ( A ) Phylogenetic tree of ECH genes homologous to Sl-AECH1 . Genes colored with orange and labeled with orange rectangles are from the syntenic regions of Solanaceae species shown in panel ( B ). Genes marked with stars have been tested involved in acylsugar biosynthesis. ( B ) The acylsugar gene cluster syntenic regions of 11 Solanaceae species and two outgroup species Ipomea trifida (Convolvulaceae) and Coffea canephora (Rubiaceae). ( C ) Reconciled evolutionary history of ECH enzyme based on panel ( A ) and ( B ). The colors of the branches correspond to different lineages shown in panel A. Grey branch means enzymes from that lineage could not be found through BLAST and may have been lost. Numbers in the circle indicate the nodes in the phylogenetic tree as shown in panel ( A ). The inferred evolutionary events were shown next to the nodes. Grey box highlighted the evolutionary history of the genes in the syntenic regions. Before the Solanaceae specific WGD events, an ECH was inserted into the syntenic region through unknown mechanism. After the WGD events, there was one ECH gene in each syntenic region on Chr07 and Chr12. Before the divergence of Solanum , Nicotiana , and Petunia species, the ECH gene on Chr07 had experienced a tandem duplication event, leading to two branches on the phylogenetic tree. During the speciation, the ECH gene on Chr12 was deleted from the genome in the most recent common ancestor of Nicotiana and Solanum after divergent from Petunia , while one of the tandem duplicates on Chr07 was lost in Petunia .

    Article Snippet: Synteny scan Protein sequences of annotated genes and the corresponding annotation files in General Feature Format (GFF) of 11 Solanaceae species, Ipomoea trifida, and Coffea canephora were downloaded from National Center for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov/genome/ ) or Solanaceae Genomics Network (SGN, https://solgenomics.net/ ).

    Techniques: Labeling

    Phylogenetic analysis of the BAHD acyltransferase. The BAHD acyltransferase pseudogene ( Cc-BAHD-pseu ) in the corresponding syntenic region ( Figure 6 ) of Coffea canephora is one of the closest Coffea sequences sister to the ASAT clade. It indicates that the BAHD acyltransferase gene was the first to harbor in this syntenic region before the divergence between Solanaceae and Rubiaceae. The translated amino acid sequence of Cc-BAHD-pseu was aligned with sequences used in Figure 6A of a previous study ( Moghe et al., 2017 ) using MUSCLE. The phylogenetic trees were built using the maximum likelihood method with 1000 bootstrap replicates. The tree was generated using RAxML/8.0.6 with the following parameters: -f a -x 12345 p 12345 -# 1000 m PROTGAMMAAUTO --auto-prot=bic , and was shown with the midpoint rooting. Genes colored with green are from the focused syntenic regions. Genes marked with stars have been biochemically tested involved in acylsugar biosynthesis in previous studies.

    Journal: eLife

    Article Title: Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity

    doi: 10.7554/eLife.56717

    Figure Lengend Snippet: Phylogenetic analysis of the BAHD acyltransferase. The BAHD acyltransferase pseudogene ( Cc-BAHD-pseu ) in the corresponding syntenic region ( Figure 6 ) of Coffea canephora is one of the closest Coffea sequences sister to the ASAT clade. It indicates that the BAHD acyltransferase gene was the first to harbor in this syntenic region before the divergence between Solanaceae and Rubiaceae. The translated amino acid sequence of Cc-BAHD-pseu was aligned with sequences used in Figure 6A of a previous study ( Moghe et al., 2017 ) using MUSCLE. The phylogenetic trees were built using the maximum likelihood method with 1000 bootstrap replicates. The tree was generated using RAxML/8.0.6 with the following parameters: -f a -x 12345 p 12345 -# 1000 m PROTGAMMAAUTO --auto-prot=bic , and was shown with the midpoint rooting. Genes colored with green are from the focused syntenic regions. Genes marked with stars have been biochemically tested involved in acylsugar biosynthesis in previous studies.

    Article Snippet: Synteny scan Protein sequences of annotated genes and the corresponding annotation files in General Feature Format (GFF) of 11 Solanaceae species, Ipomoea trifida, and Coffea canephora were downloaded from National Center for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov/genome/ ) or Solanaceae Genomics Network (SGN, https://solgenomics.net/ ).

    Techniques: Sequencing, Generated

    Analysis of the evolutionary history of the ACS genes in the syntenic regions in different Solanaceae species. ( A ) Phylogenetic tree of ACS genes homologous to Sl-AACS1 . Genes colored with blue and labeled with blue rectangles are from the syntenic regions of Solanaceae species shown in panel ( B ). Genes marked with stars have been tested involved in acylsugar biosynthesis. ( B ) The acylsugar gene cluster syntenic regions of 11 Solanaceae species and two outgroup species Ipomea trifida (Convolvulaceae) and Coffea canephora (Rubiaceae). ( C ) Reconciled evolutionary history of ACS enzyme based on panel ( A ) and ( B ). The colors of the branches correspond to different lineages shown in panel ( A ). Grey branch means enzymes from that lineage could not be found through BLAST and may have been lost. Numbers in the circle indicate the nodes in the phylogenetic tree as shown in panel A. The inferred evolutionary events were shown next to the nodes. A tandem duplication event happened before the Solanaceae specific WGD events, leading to two adjacent ACS genes on Chr02 ( Solyc02g082880 and Solyc02g082870 ), which were placed on two independent lineages in the phylogenetic tree. Solyc02g082870 had gone through two rounds of WGD events, supported by the observation that Solyc02g082870 and Solyc03g032210 are located in corresponding syntenic blocks. Solyc02g082880 may have experienced the segmental duplication, resulting in the ACS gene on Chr07, which had experienced another two rounds of tandem duplication in the common ancestor of Solanum species ( Sl-AACS1 , Solyc07g043660 , and Solyc07g043640 ). However, whether the segmental duplication event happened before or after the Solanaceae specific WGD events cannot be well resolved by the phylogenetic analysis. Two hypotheses were proposed as shown in the grey boxes. If the insertion happened before WGD, two independent gene loss events on chromosomes 7 and 12 should have happened in Petunia (Hypothesis 2). If the insertion happened after WGD, only one gene loss in Petunia was supposed to have happened (Hypothesis 1). Note that node 4 in ( A ) leads to two clades, one without any Petunia ACS homolog (darker blue) and the other with Petunia homologs (cyan). With regard to the timing of the duplication event leading to these two clades, it was likely before the split between the Petunia and the tomato/tobacco lineages where one Petunia loss event occurred (darker blue). If it was after the split, the presence of a Petunia gene would need to be explained by a gene gain through horizontal gene transfer or other means (cyan) - a far less likely scenario than a gene loss.

    Journal: eLife

    Article Title: Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity

    doi: 10.7554/eLife.56717

    Figure Lengend Snippet: Analysis of the evolutionary history of the ACS genes in the syntenic regions in different Solanaceae species. ( A ) Phylogenetic tree of ACS genes homologous to Sl-AACS1 . Genes colored with blue and labeled with blue rectangles are from the syntenic regions of Solanaceae species shown in panel ( B ). Genes marked with stars have been tested involved in acylsugar biosynthesis. ( B ) The acylsugar gene cluster syntenic regions of 11 Solanaceae species and two outgroup species Ipomea trifida (Convolvulaceae) and Coffea canephora (Rubiaceae). ( C ) Reconciled evolutionary history of ACS enzyme based on panel ( A ) and ( B ). The colors of the branches correspond to different lineages shown in panel ( A ). Grey branch means enzymes from that lineage could not be found through BLAST and may have been lost. Numbers in the circle indicate the nodes in the phylogenetic tree as shown in panel A. The inferred evolutionary events were shown next to the nodes. A tandem duplication event happened before the Solanaceae specific WGD events, leading to two adjacent ACS genes on Chr02 ( Solyc02g082880 and Solyc02g082870 ), which were placed on two independent lineages in the phylogenetic tree. Solyc02g082870 had gone through two rounds of WGD events, supported by the observation that Solyc02g082870 and Solyc03g032210 are located in corresponding syntenic blocks. Solyc02g082880 may have experienced the segmental duplication, resulting in the ACS gene on Chr07, which had experienced another two rounds of tandem duplication in the common ancestor of Solanum species ( Sl-AACS1 , Solyc07g043660 , and Solyc07g043640 ). However, whether the segmental duplication event happened before or after the Solanaceae specific WGD events cannot be well resolved by the phylogenetic analysis. Two hypotheses were proposed as shown in the grey boxes. If the insertion happened before WGD, two independent gene loss events on chromosomes 7 and 12 should have happened in Petunia (Hypothesis 2). If the insertion happened after WGD, only one gene loss in Petunia was supposed to have happened (Hypothesis 1). Note that node 4 in ( A ) leads to two clades, one without any Petunia ACS homolog (darker blue) and the other with Petunia homologs (cyan). With regard to the timing of the duplication event leading to these two clades, it was likely before the split between the Petunia and the tomato/tobacco lineages where one Petunia loss event occurred (darker blue). If it was after the split, the presence of a Petunia gene would need to be explained by a gene gain through horizontal gene transfer or other means (cyan) - a far less likely scenario than a gene loss.

    Article Snippet: Synteny scan Protein sequences of annotated genes and the corresponding annotation files in General Feature Format (GFF) of 11 Solanaceae species, Ipomoea trifida, and Coffea canephora were downloaded from National Center for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov/genome/ ) or Solanaceae Genomics Network (SGN, https://solgenomics.net/ ).

    Techniques: Labeling

    Analysis of the evolutionary history of the BAHD acyltransferases in the syntenic regions in different Solanaceae species. ( A ) Phylogenetic tree of BAHD acyltransferases homologous to Solyc07g043670. Genes colored with green and labeled with green rectangles are from the syntenic regions of Solanaceae species shown in panel ( B ). Genes marked with stars have been biochemically tested involved in acylsugar biosynthesis in previous studies. ( B ) The acylsugar gene cluster syntenic regions of 11 Solanaceae species and two outgroup species Ipomea trifida (Convolvulaceae) and Coffea canephora (Rubiaceae). ( C ) Reconciled evolutionary history of BAHD acyltransferases based on panel ( A ) and ( B ). The colors of the branches correspond to different lineages shown in panel ( A ). Grey branch means enzymes from that lineage could not be found through BLAST and may have been lost. Numbers in the circle indicate the nodes in the phylogenetic tree as shown in panel A. The inferred evolutionary events were shown next to the nodes. Grey box highlighted the evolutionary history of the genes in the syntenic region. Before the Solanaceae specific whole genome duplication (WGD) events, the BAHD acyltransferase gene was tandemly duplicated. The WGD events resulted in at least two genomic regions (Chr07 and Chr12), each containing two BAHD acyltransferase genes. Before the divergence of Solanum , Nicotiana , and Petunia species, one of the tandem copies in Chr12 region was lost, and only orthologs of Sl-ASAT1 was retained. The question mark next to Petunia denotes the inconsistence of the phylogenetic relationship and the chromosome location of the gene Pa-B816 with an unknown mechanism.

    Journal: eLife

    Article Title: Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity

    doi: 10.7554/eLife.56717

    Figure Lengend Snippet: Analysis of the evolutionary history of the BAHD acyltransferases in the syntenic regions in different Solanaceae species. ( A ) Phylogenetic tree of BAHD acyltransferases homologous to Solyc07g043670. Genes colored with green and labeled with green rectangles are from the syntenic regions of Solanaceae species shown in panel ( B ). Genes marked with stars have been biochemically tested involved in acylsugar biosynthesis in previous studies. ( B ) The acylsugar gene cluster syntenic regions of 11 Solanaceae species and two outgroup species Ipomea trifida (Convolvulaceae) and Coffea canephora (Rubiaceae). ( C ) Reconciled evolutionary history of BAHD acyltransferases based on panel ( A ) and ( B ). The colors of the branches correspond to different lineages shown in panel ( A ). Grey branch means enzymes from that lineage could not be found through BLAST and may have been lost. Numbers in the circle indicate the nodes in the phylogenetic tree as shown in panel A. The inferred evolutionary events were shown next to the nodes. Grey box highlighted the evolutionary history of the genes in the syntenic region. Before the Solanaceae specific whole genome duplication (WGD) events, the BAHD acyltransferase gene was tandemly duplicated. The WGD events resulted in at least two genomic regions (Chr07 and Chr12), each containing two BAHD acyltransferase genes. Before the divergence of Solanum , Nicotiana , and Petunia species, one of the tandem copies in Chr12 region was lost, and only orthologs of Sl-ASAT1 was retained. The question mark next to Petunia denotes the inconsistence of the phylogenetic relationship and the chromosome location of the gene Pa-B816 with an unknown mechanism.

    Article Snippet: Synteny scan Protein sequences of annotated genes and the corresponding annotation files in General Feature Format (GFF) of 11 Solanaceae species, Ipomoea trifida, and Coffea canephora were downloaded from National Center for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov/genome/ ) or Solanaceae Genomics Network (SGN, https://solgenomics.net/ ).

    Techniques: Labeling

    Quantitative RT-PCR validation of DGE analysis. Relative quantification was carried out to measure changes of selective WRKY gene expression in P . coffeae resistant and susceptible root sample relative to an endogenous reference gene (RPS2). Red line shows the expression analysis in DGE. Data (technical triplicates of three biological experiments) are reported as means ± standard error.

    Journal: PLoS ONE

    Article Title: Evolutionary Expansion of WRKY Gene Family in Banana and Its Expression Profile during the Infection of Root Lesion Nematode, Pratylenchus coffeae

    doi: 10.1371/journal.pone.0162013

    Figure Lengend Snippet: Quantitative RT-PCR validation of DGE analysis. Relative quantification was carried out to measure changes of selective WRKY gene expression in P . coffeae resistant and susceptible root sample relative to an endogenous reference gene (RPS2). Red line shows the expression analysis in DGE. Data (technical triplicates of three biological experiments) are reported as means ± standard error.

    Article Snippet: To gain an insight into nematode-Musa interactions, genome-wide expression pattern of MusaWRKY in both nematode resistant and susceptible cultivars were analyzed during the infection of a mixed life stage population of P . coffeae , by performing Illumina sequencing.

    Techniques: Quantitative RT-PCR, Expressing

    Time-course expression profiles of 8 defence-related genes in ramie roots during incompatible (●) and compatible (Δ) interactions with P. coffeae revealed by qRT-PCR analyses. ( a ) TI , Trypsin inhibitor; ( b ) PI , Proteinase inhibitor; ( c ) CPI , Cysteine protease inhibitor; ( d ) SOD , Superoxide dismutase; ( e ) PPO , Polyphenoloxidase; ( f ) CHI , Chitinase; ( g ) ERF , Ethylene-responsive transcription factor; and ( h ) LOX , Lipoxygenase. Data from qRT-PCR are means of three biological replicates (each has 2 experimental replicates) and bars represent standerd error.

    Journal: International Journal of Molecular Sciences

    Article Title: Identification of Ramie Genes in Response to Pratylenchus coffeae Infection Challenge by Digital Gene Expression Analysis

    doi: 10.3390/ijms160921989

    Figure Lengend Snippet: Time-course expression profiles of 8 defence-related genes in ramie roots during incompatible (●) and compatible (Δ) interactions with P. coffeae revealed by qRT-PCR analyses. ( a ) TI , Trypsin inhibitor; ( b ) PI , Proteinase inhibitor; ( c ) CPI , Cysteine protease inhibitor; ( d ) SOD , Superoxide dismutase; ( e ) PPO , Polyphenoloxidase; ( f ) CHI , Chitinase; ( g ) ERF , Ethylene-responsive transcription factor; and ( h ) LOX , Lipoxygenase. Data from qRT-PCR are means of three biological replicates (each has 2 experimental replicates) and bars represent standerd error.

    Article Snippet: During the early stage of root challenge by P. coffeae , 137 DEGs of ramie were induced, and DGE analysis revealed most of them (85.4%) to be upregulated.

    Techniques: Expressing, Quantitative RT-PCR, Protease Inhibitor