pubmed.ncbi.nlm.nih.gov

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

  • ️Thu Jan 01 2015

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

Chen Jiao et al. BMC Genomics. 2015.

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.

PubMed Disclaimer

Figures

Figure 1
Figure 1

Mapping of de novo assembled transcripts of the three Chinese wild Vitis, 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”.

Figure 2
Figure 2

Distinct genes in the three Chinese wild Vitis , BH, HN and S. (A) Number of distinct protein-coding genes and non-coding transcripts from de novo transcriptome assemblies of the three Chinese Vitis leaf tissues, which were collected at 0, 6, 12, 24, 48, 72, 96, and 120 hours post inoculation with PM, respectively. (B) Venn diagram of GO terms enriched in the distinct protein-coding genes. (C) Number of distinct genes encoding disease resistance proteins, receptor like kinases and transcription factors. BH, V. pseudoreticulata accession “Baihe-13-1”; HN, V. pseudoreticulata accession “Hunan-1”; S, V. quinquangularis accession “Shang-24”.

Figure 3
Figure 3

SNPs and small indels between the three Chinese wild Vitis , 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”.

Similar articles

Cited by

References

    1. FAOSTAT. http://faostat3.fao.org/
    1. Owens CL. Grapes. In: Hancock J, editor. Temperate Fruit Crop Breeding. Netherlands: Springer; 2008. pp. 197–233.
    1. Doster MA, Schnathorst WC. Comparative susceptibility of various grapevine cultivars to the powdery mildew fungus Uncinula necator. Am J Enol Viticult. 1985;36:101–104.
    1. Langcake P, Lovell PA. Light and electron microscopical studies of the infection of Vitis spp by Plasmopara viticola, the downy mildew pathogen. Vitis. 1980;19:321–337.
    1. Mortensen JA. Sources and inheritance of resistance to anthracnose in Vitis. J Hered. 1981;72:423–426.

Publication types

MeSH terms

LinkOut - more resources