Limits...
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.

Show MeSH

Related in: MedlinePlus

Mapping ofde novoassembled transcripts of the three Chinese wildVitis, BH (A), HN (B), and S (C), to the reference PN40024 genome. No mapping: Contigs not mapped; Multiple hits: Contigs mapped to multiple genomic locations; Unique hit: Contigs mapped to unique genomic locations; Mapping in intergenic regions: Contigs mapped to intergenic regions; Small overlap with gene regions: Contigs mapped to gene regions with low overlapping (<90% of contig length); Large overlap with gene regions (+): Contigs mapped to gene regions in sense directions with high overlapping (≥90% of contig length) ; Large overlap with gene regions (−): Contigs mapped to gene regions in antisense directions with high overlapping (≥90% of contig length). 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
getmorefigures.php?uid=PMC4373064&req=5

Fig1: Mapping ofde novoassembled transcripts of the three Chinese wildVitis, BH (A), HN (B), and S (C), to the reference PN40024 genome. No mapping: Contigs not mapped; Multiple hits: Contigs mapped to multiple genomic locations; Unique hit: Contigs mapped to unique genomic locations; Mapping in intergenic regions: Contigs mapped to intergenic regions; Small overlap with gene regions: Contigs mapped to gene regions with low overlapping (<90% of contig length); Large overlap with gene regions (+): Contigs mapped to gene regions in sense directions with high overlapping (≥90% of contig length) ; Large overlap with gene regions (−): Contigs mapped to gene regions in antisense directions with high overlapping (≥90% of contig length). BH, V. pseudoreticulata accession “Baihe-13-1”; HN, V. pseudoreticulata accession “Hunan-1”; S, V. quinquangularis accession “Shang-24”.

Mentions: To discover the variations between Chinese wild Vitis and PN40024, a genotype derived from Pinot Noir, all three transcriptomes were aligned to the PN40024 genome. There were 94% (32,892), 94% (36,151) and 93% (35,589) of the total transcripts can be uniquely aligned to the reference genome with ≥ 97% sequence identity for BH, HN and S, respectively (Figure 1). Only 1% of them were mapped to multiple locations of the PN40024 genome and most of them were mapped to two locations. The majority of transcripts (83%, 82% and 80% of the total transcripts from BH, HN and S, respectively) were mapped to the annotated gene regions (version 12× V0) with overlap fraction ≥ 90% and had the same strand with the corresponding PN40024 transcripts; whereas around 2% of the transcripts were aligned to gene regions in antisense orientations. Notably, a small proportion (5-7%) of the transcripts were aligned entirely to the intergenic regions. Among all the assembled transcripts, 1,758 (5%, BH), 2,083 (5%, HN) and 2,331 (6%, S) could not be aligned to the PN40024 genome. We considered these transcripts as candidates for distinct genes.Figure 1


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)

Mapping ofde novoassembled transcripts of the three Chinese wildVitis, BH (A), HN (B), and S (C), to the reference PN40024 genome. No mapping: Contigs not mapped; Multiple hits: Contigs mapped to multiple genomic locations; Unique hit: Contigs mapped to unique genomic locations; Mapping in intergenic regions: Contigs mapped to intergenic regions; Small overlap with gene regions: Contigs mapped to gene regions with low overlapping (<90% of contig length); Large overlap with gene regions (+): Contigs mapped to gene regions in sense directions with high overlapping (≥90% of contig length) ; Large overlap with gene regions (−): Contigs mapped to gene regions in antisense directions with high overlapping (≥90% of contig length). 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

Fig1: Mapping ofde novoassembled transcripts of the three Chinese wildVitis, BH (A), HN (B), and S (C), to the reference PN40024 genome. No mapping: Contigs not mapped; Multiple hits: Contigs mapped to multiple genomic locations; Unique hit: Contigs mapped to unique genomic locations; Mapping in intergenic regions: Contigs mapped to intergenic regions; Small overlap with gene regions: Contigs mapped to gene regions with low overlapping (<90% of contig length); Large overlap with gene regions (+): Contigs mapped to gene regions in sense directions with high overlapping (≥90% of contig length) ; Large overlap with gene regions (−): Contigs mapped to gene regions in antisense directions with high overlapping (≥90% of contig length). BH, V. pseudoreticulata accession “Baihe-13-1”; HN, V. pseudoreticulata accession “Hunan-1”; S, V. quinquangularis accession “Shang-24”.
Mentions: To discover the variations between Chinese wild Vitis and PN40024, a genotype derived from Pinot Noir, all three transcriptomes were aligned to the PN40024 genome. There were 94% (32,892), 94% (36,151) and 93% (35,589) of the total transcripts can be uniquely aligned to the reference genome with ≥ 97% sequence identity for BH, HN and S, respectively (Figure 1). Only 1% of them were mapped to multiple locations of the PN40024 genome and most of them were mapped to two locations. The majority of transcripts (83%, 82% and 80% of the total transcripts from BH, HN and S, respectively) were mapped to the annotated gene regions (version 12× V0) with overlap fraction ≥ 90% and had the same strand with the corresponding PN40024 transcripts; whereas around 2% of the transcripts were aligned to gene regions in antisense orientations. Notably, a small proportion (5-7%) of the transcripts were aligned entirely to the intergenic regions. Among all the assembled transcripts, 1,758 (5%, BH), 2,083 (5%, HN) and 2,331 (6%, S) could not be aligned to the PN40024 genome. We considered these transcripts as candidates for distinct genes.Figure 1

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