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Transcriptome characterization of three wild Chinese Vitis uncovers a large number of distinct disease related genes.

Jiao C, Gao M, Wang X, Fei Z - BMC Genomics (2015)

Bottom Line: These transcripts were significantly enriched with genes involved in secondary metabolisms and plant responses to abiotic stresses.The three de novo assembled transcriptomes provide a comprehensive sequence resource for molecular genetic research in grape.Furthermore, we identified hundreds of cis-NAT pairs which showed their potential regulatory roles in secondary metabolism and abiotic stress responses.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China. cj334@cornell.edu.

ABSTRACT

Background: Grape is one of the most valuable fruit crops and can serve for both fresh consumption and wine production. Grape cultivars have been selected and evolved to produce high-quality fruits during their domestication over thousands of years. However, current widely planted grape cultivars suffer extensive loss to many diseases while most wild species show resistance to various pathogens. Therefore, a comprehensive evaluation of wild grapes would contribute to the improvement of disease resistance in grape breeding programs.

Results: We performed deep transcriptome sequencing of three Chinese wild grapes using the Illumina strand-specific RNA-Seq technology. High quality transcriptomes were assembled de novo and more than 93% transcripts were shared with the reference PN40024 genome. Over 1,600 distinct transcripts, which were absent or highly divergent from sequences in the reference PN40024 genome, were identified in each of the three wild grapes, among which more than 1,000 were potential protein-coding genes. Gene Ontology (GO) and pathway annotations of these distinct genes showed those involved in defense responses and plant secondary metabolisms were highly enriched. More than 87,000 single nucleotide polymorphisms (SNPs) and 2,000 small insertions or deletions (indels) were identified between each genotype and PN40024, and approximately 20% of the SNPs caused nonsynonymous mutations. Finally, we discovered 100 to 200 highly confident cis-natural antisense transcript (cis-NAT) pairs in each genotype. These transcripts were significantly enriched with genes involved in secondary metabolisms and plant responses to abiotic stresses.

Conclusion: The three de novo assembled transcriptomes provide a comprehensive sequence resource for molecular genetic research in grape. The newly discovered genes from wild Vitis, as well as SNPs and small indels we identified, may facilitate future studies on the molecular mechanisms related to valuable traits possessed by these wild Vitis and contribute to the grape breeding programs. Furthermore, we identified hundreds of cis-NAT pairs which showed their potential regulatory roles in secondary metabolism and abiotic stress responses.

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SNPs and small indels between the three Chinese wildVitis, BH, HN and S, and PN40024. (A) Number of SNPs at different annotated regions of the reference PN40024 genome. (B) Number of small indels at different annotated regions of the reference PN40024 genome. (C) Number of genes affected by SNPs and small indels. SSA/D, splice site acceptor or splice site donor; FS, frame shift; SpG, stop codon gained; SpL, stop codon lost; StL, start codon lost. BH, V. pseudoreticulata accession “Baihe-13-1”; HN, V. pseudoreticulata accession “Hunan-1”; S, V. quinquangularis accession “Shang-24”.
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Fig3: SNPs and small indels between the three Chinese wildVitis, BH, HN and S, and PN40024. (A) Number of SNPs at different annotated regions of the reference PN40024 genome. (B) Number of small indels at different annotated regions of the reference PN40024 genome. (C) Number of genes affected by SNPs and small indels. SSA/D, splice site acceptor or splice site donor; FS, frame shift; SpG, stop codon gained; SpL, stop codon lost; StL, start codon lost. BH, V. pseudoreticulata accession “Baihe-13-1”; HN, V. pseudoreticulata accession “Hunan-1”; S, V. quinquangularis accession “Shang-24”.

Mentions: Genomic variations, such as SNPs and small insertions and deletions (indels) are important driving force of genetic diversity. We identified SNPs and small indels through mapping the RNA-Seq reads from each accession to the reference PN40024 genome. We obtained a total of 110,450 SNPs and 2,354 small indels between BH and PN40024, 87,583 SNPs and 2,079 small indels between HN and PN40024, and 89,024 SNPs and 2,085 small indels between S and PN40024. Among these variations, 52% (BH), 48% (HN) and 49% (S) of SNPs, and 3.19% (BH), 3.56% (HN) and 4.22% (S) of small indels were located in the annotated coding regions (Figure 3A and 3B). In BH, we identified ~24,000 nonsynonymous substitutions, which potentially affect approximately 10,000 genes. In the other two accessions, we detected more than 18,000 nonsynonymous mutations that may alter the function of ~9,000 genes. The overall ratio of nonsynonymous to synonymous sites was ~0.7 in all three accessions. Interestingly, this ratio in NBS-LRR genes was substantially higher (1.3 in BH, 2.1 in HN and 3.0 in S). SNPs located at specific regions might have large effects on corresponding genes, such as gain or loss of start/stop codons, and disruption of splice site acceptors or donors [47,48]. We found 32, 24 and 24 genes in BH, HN and S, respectively, contained loss of start codon SNPs which would change the length of protein products (Figure 3C). About 40 genes with loss of stop codons and 70 genes with gain of stop codons were identified in each accession. Moreover, small indels mapped to coding regions (Figure 3B) led to the frame shifts of 74, 72 and 87 genes in BH, HN and S, respectively (Figure 3C). The identified SNPs and small indels were listed in Additional file 4.Figure 3


Transcriptome characterization of three wild Chinese Vitis uncovers a large number of distinct disease related genes.

Jiao C, Gao M, Wang X, Fei Z - BMC Genomics (2015)

SNPs and small indels between the three Chinese wildVitis, BH, HN and S, and PN40024. (A) Number of SNPs at different annotated regions of the reference PN40024 genome. (B) Number of small indels at different annotated regions of the reference PN40024 genome. (C) Number of genes affected by SNPs and small indels. SSA/D, splice site acceptor or splice site donor; FS, frame shift; SpG, stop codon gained; SpL, stop codon lost; StL, start codon lost. BH, V. pseudoreticulata accession “Baihe-13-1”; HN, V. pseudoreticulata accession “Hunan-1”; S, V. quinquangularis accession “Shang-24”.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4373064&req=5

Fig3: SNPs and small indels between the three Chinese wildVitis, BH, HN and S, and PN40024. (A) Number of SNPs at different annotated regions of the reference PN40024 genome. (B) Number of small indels at different annotated regions of the reference PN40024 genome. (C) Number of genes affected by SNPs and small indels. SSA/D, splice site acceptor or splice site donor; FS, frame shift; SpG, stop codon gained; SpL, stop codon lost; StL, start codon lost. BH, V. pseudoreticulata accession “Baihe-13-1”; HN, V. pseudoreticulata accession “Hunan-1”; S, V. quinquangularis accession “Shang-24”.
Mentions: Genomic variations, such as SNPs and small insertions and deletions (indels) are important driving force of genetic diversity. We identified SNPs and small indels through mapping the RNA-Seq reads from each accession to the reference PN40024 genome. We obtained a total of 110,450 SNPs and 2,354 small indels between BH and PN40024, 87,583 SNPs and 2,079 small indels between HN and PN40024, and 89,024 SNPs and 2,085 small indels between S and PN40024. Among these variations, 52% (BH), 48% (HN) and 49% (S) of SNPs, and 3.19% (BH), 3.56% (HN) and 4.22% (S) of small indels were located in the annotated coding regions (Figure 3A and 3B). In BH, we identified ~24,000 nonsynonymous substitutions, which potentially affect approximately 10,000 genes. In the other two accessions, we detected more than 18,000 nonsynonymous mutations that may alter the function of ~9,000 genes. The overall ratio of nonsynonymous to synonymous sites was ~0.7 in all three accessions. Interestingly, this ratio in NBS-LRR genes was substantially higher (1.3 in BH, 2.1 in HN and 3.0 in S). SNPs located at specific regions might have large effects on corresponding genes, such as gain or loss of start/stop codons, and disruption of splice site acceptors or donors [47,48]. We found 32, 24 and 24 genes in BH, HN and S, respectively, contained loss of start codon SNPs which would change the length of protein products (Figure 3C). About 40 genes with loss of stop codons and 70 genes with gain of stop codons were identified in each accession. Moreover, small indels mapped to coding regions (Figure 3B) led to the frame shifts of 74, 72 and 87 genes in BH, HN and S, respectively (Figure 3C). The identified SNPs and small indels were listed in Additional file 4.Figure 3

Bottom Line: These transcripts were significantly enriched with genes involved in secondary metabolisms and plant responses to abiotic stresses.The three de novo assembled transcriptomes provide a comprehensive sequence resource for molecular genetic research in grape.Furthermore, we identified hundreds of cis-NAT pairs which showed their potential regulatory roles in secondary metabolism and abiotic stress responses.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China. cj334@cornell.edu.

ABSTRACT

Background: Grape is one of the most valuable fruit crops and can serve for both fresh consumption and wine production. Grape cultivars have been selected and evolved to produce high-quality fruits during their domestication over thousands of years. However, current widely planted grape cultivars suffer extensive loss to many diseases while most wild species show resistance to various pathogens. Therefore, a comprehensive evaluation of wild grapes would contribute to the improvement of disease resistance in grape breeding programs.

Results: We performed deep transcriptome sequencing of three Chinese wild grapes using the Illumina strand-specific RNA-Seq technology. High quality transcriptomes were assembled de novo and more than 93% transcripts were shared with the reference PN40024 genome. Over 1,600 distinct transcripts, which were absent or highly divergent from sequences in the reference PN40024 genome, were identified in each of the three wild grapes, among which more than 1,000 were potential protein-coding genes. Gene Ontology (GO) and pathway annotations of these distinct genes showed those involved in defense responses and plant secondary metabolisms were highly enriched. More than 87,000 single nucleotide polymorphisms (SNPs) and 2,000 small insertions or deletions (indels) were identified between each genotype and PN40024, and approximately 20% of the SNPs caused nonsynonymous mutations. Finally, we discovered 100 to 200 highly confident cis-natural antisense transcript (cis-NAT) pairs in each genotype. These transcripts were significantly enriched with genes involved in secondary metabolisms and plant responses to abiotic stresses.

Conclusion: The three de novo assembled transcriptomes provide a comprehensive sequence resource for molecular genetic research in grape. The newly discovered genes from wild Vitis, as well as SNPs and small indels we identified, may facilitate future studies on the molecular mechanisms related to valuable traits possessed by these wild Vitis and contribute to the grape breeding programs. Furthermore, we identified hundreds of cis-NAT pairs which showed their potential regulatory roles in secondary metabolism and abiotic stress responses.

Show MeSH
Related in: MedlinePlus