Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.).
Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.).
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DOI：
10.1093/dnares/dsu035
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发表时间：
2015-02
期刊：
影响因子：
--
通讯作者：
Choi D
中科院分区：
文献类型：
--
作者：
Kim S;Kim MS;Kim YM;Yeom SI;Cheong K;Kim KT;Jeon J;Kim S;Kim DS;Sohn SH;Lee YH;Choi D
洋葱（Allium cepa L.）是世界上种植和消费最广泛的蔬菜作物之一。尽管大量洋葱转录组数据已存入公共数据库，但由于非编码序列与编码序列混合，蛋白质编码基因的序列不够准确，无法使用。我们使用集成结构基因注释管道 (ISGAP) 从头序列组装和密集结构注释生成了高质量、带注释的洋葱转录组，通过消除内含子序列，在 165,179 个组装的转录本中鉴定了 54,165 个蛋白质编码基因，总大小为 203.0 Mb。 ISGAP 进行了可靠的注释，根据参考蛋白识别准确的基因结构，以及组装转录本的从头开始基因模型。综合功能注释和基于基因的 SNP 分析揭示了洋葱的基因和转录组变异的完整生物学库。本研究开发的方法为仅基于从头转录组数据构建生物体参考基因集提供了强大的工具。此外，此处描述的洋葱参考基因及其变异代表了葱属植物分子育种和基因克隆的重要工具。
The onion (Allium cepa L.) is one of the most widely cultivated and consumed vegetable crops in the world. Although a considerable amount of onion transcriptome data has been deposited into public databases, the sequences of the protein-coding genes are not accurate enough to be used, owing to non-coding sequences intermixed with the coding sequences. We generated a high-quality, annotated onion transcriptome from de novo sequence assembly and intensive structural annotation using the integrated structural gene annotation pipeline (ISGAP), which identified 54,165 protein-coding genes among 165,179 assembled transcripts totalling 203.0 Mb by eliminating the intron sequences. ISGAP performed reliable annotation, recognizing accurate gene structures based on reference proteins, and ab initio gene models of the assembled transcripts. Integrative functional annotation and gene-based SNP analysis revealed a whole biological repertoire of genes and transcriptomic variation in the onion. The method developed in this study provides a powerful tool for the construction of reference gene sets for organisms based solely on de novo transcriptome data. Furthermore, the reference genes and their variation described here for the onion represent essential tools for molecular breeding and gene cloning in Allium spp.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
4.4
作者：
Annadurai RS;Jayakumar V;Mugasimangalam RC;Katta MA;Anand S;Gopinathan S;Sarma SP;Fernandes SJ;Mullapudi N;Murugesan S;Rao SN
通讯作者：
Rao SN
影响因子：
12.3
作者：
Denoeud F;Aury JM;Da Silva C;Noel B;Rogier O;Delledonne M;Morgante M;Valle G;Wincker P;Scarpelli C;Jaillon O;Artiguenave F
通讯作者：
Artiguenave F
影响因子：
4.4
作者：
Ashrafi H;Hill T;Stoffel K;Kozik A;Yao J;Chin-Wo SR;Van Deynze A
通讯作者：
Van Deynze A
影响因子：
64.8
作者：
通讯作者：
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