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

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• 作者：Chen Jiao (1) (2) (3)
  Min Gao (1) (2)
  Xiping Wang (1) (2)
  Zhangjun Fei (3) (4)
  
  1. State Key Laboratory of Crop Stress Biology in Arid Areas ; College of Horticulture ; Northwest A&F University ; Yangling ; Shaanxi ; 712100 ; China
  2. Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China ; Ministry of Agriculture ; Northwest A&F University ; Yangling ; Shaanxi ; 712100 ; China
  3. Boyce Thompson Institute for Plant Research ; Cornell University ; Ithaca ; NY ; 14853 ; USA
  4. USDA Robert W. Holley Center for Agriculture and Health ; Tower Road ; Ithaca ; NY ; 14853 ; USA
  
• 关键词：Grape ; Chinese wild Vitis ; De novo transcriptome ; Disease related genes ; Cis ; NATs
• 刊名：BMC Genomics
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：16
• 期：1
• 全文大小：1,481 KB
• 参考文献：1. FAOSTAT. http://faostat3.fao.org/
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• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

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.