Transcriptome characterization of three wild Chinese Vitis uncovers a large number of distinct disease related genes.
Transcriptome characterization of three wild Chinese Vitis uncovers a large number of distinct disease related genes.
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三种野生中国葡萄的转录组特征揭示了大量不同的疾病相关基因
DOI：
10.1186/s12864-015-1442-3
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发表时间：
2015-03-21
期刊：
影响因子：
4.4
通讯作者：
Fei Z
中科院分区：
文献类型：
--
作者：
Jiao C;Gao M;Wang X;Fei Z
背景：葡萄是最有价值的水果作物之一，可用于新鲜食用和葡萄酒生产。葡萄品种在数千年的驯化过程中被选择和进化以生产高品质的水果。然而，目前广泛种植的葡萄品种遭受许多疾病的广泛损失，而大多数野生物种对各种病原体表现出抗性。因此，对野生葡萄进行综合评价，有助于葡萄抗病育种工作的开展。结果：利用Illumina strand-specific RNA-Seq技术对3个中国野生葡萄进行了深度转录组测序。从头组装高质量的转录组，并且超过93%的转录物与参考PN 40024基因组共享。在三种野生葡萄中的每一种中鉴定了超过1，600种不同的转录物，这些转录物与参考PN 40024基因组中的序列不存在或高度不同，其中超过1，000种是潜在的蛋白质编码基因。基因本体（GO）和这些不同的基因的途径注释表明，参与防御反应和植物次生代谢的高度富集。在每个基因型和PN 40024之间确定了超过87，000个单核苷酸多态性（SNP）和2，000个小插入或缺失（indels），大约20%的SNP引起非同义突变。最后，我们发现了100至200个高度可信的顺式-天然反义转录本（cis-NAT）对在每个基因型。这些转录本中含有丰富的参与次生代谢和植物对非生物stress.Conclusion响应的基因，为葡萄的分子遗传学研究提供了一个全面的序列资源。这些新发现的野生葡萄属基因，以及我们发现的SNPs和小插入缺失，将有助于进一步研究野生葡萄属具有重要性状的分子机制，为葡萄育种提供参考。此外，我们确定了数百个顺式NAT对，显示其在次生代谢和非生物胁迫响应的潜在调控作用。
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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影响因子：
14.9
作者：
Benson DA;Cavanaugh M;Clark K;Karsch-Mizrachi I;Lipman DJ;Ostell J;Sayers EW
通讯作者：
Sayers EW
影响因子：
5.4
作者：
Barker, CL;Donald, T;Dry, I
通讯作者：
Dry, I
影响因子：
6.5
作者：
Fekete, Csaba;Fung, Raymond W. M.;Kovacs, Laszlo G.
通讯作者：
Kovacs, Laszlo G.
影响因子：
3.2
作者：
Carroll, JE;Wilcox, WF
通讯作者：
Wilcox, WF
影响因子：
5.4
作者：
Fischer, BM;Salakhutdinov, I;Zyprian, EM
通讯作者：
Zyprian, EM