De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity.
De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity.
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DOI：
10.1186/1471-2164-12-389
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发表时间：
2011-08-02
期刊：
影响因子：
4.4
通讯作者：
Simon PW
中科院分区：
文献类型：
--
作者：
Iorizzo M;Senalik DA;Grzebelus D;Bowman M;Cavagnaro PF;Matvienko M;Ashrafi H;Van Deynze A;Simon PW
在新一代测序技术中，像Illumina和SOLiD这样的平台产生的读长较短，但与454或桑格测序法相比，具有更高的覆盖度以及更低的每个测序核苷酸成本。现在的一个挑战是开发有效的策略，以便利用短读长平台进行从头组装和标记开发。本研究的范围是利用Illumina平台对多种基因型的胡萝卜表达序列标签（EST）进行从头组装，并识别多态性。
对来自四种遗传背景的转录组序列进行从头组装，产生了58751个重叠群和单一序列。这些组装序列中超过50%都有注释，从而能够检测到转座元件和新的胡萝卜花青素基因。我们的组装中存在多种遗传背景，这使得能够识别出114个通过计算得出的多态性简单重复序列（SSR），以及在20×或更高覆盖深度下的20058个单核苷酸多态性（SNP）。多态性主要存在于自交系之间，但栽培种与野生种重组自交系群体除外，该群体在样本内具有较高的多态性。大约90%的测试SSR引物和88%的测试SNP引物都扩增出了产物，其中分别有70%和46%的产物大小符合预期。在经过验证的SSR和SNP标记中，84%的SSR标记和82%的SNP标记具有多态性。在两个不同的作图群体中，大约25%进行基因分型的SNP是多态性的。
这项研究证实了短读长平台在胡萝卜表达序列标签从头组装以及遗传多态性识别方面的潜力。此外，我们生成了胡萝卜的第一个大规模转录组，胡萝卜是一个缺乏基因组资源的物种。
Among next generation sequence technologies, platforms such as Illumina and SOLiD produce short reads but with higher coverage and lower cost per sequenced nucleotide than 454 or Sanger. A challenge now is to develop efficient strategies to use short-read length platforms for de novo assembly and marker development. The scope of this study was to develop a de novo assembly of carrot ESTs from multiple genotypes using the Illumina platform, and to identify polymorphisms. A de novo assembly of transcriptome sequence from four genetic backgrounds produced 58,751 contigs and singletons. Over 50% of these assembled sequences were annotated allowing detection of transposable elements and new carrot anthocyanin genes. Presence of multiple genetic backgrounds in our assembly allowed the identification of 114 computationally polymorphic SSRs, and 20,058 SNPs at a depth of coverage of 20× or more. Polymorphisms were predominantly between inbred lines except for the cultivated x wild RIL pool which had high intra-sample polymorphism. About 90% and 88% of tested SSR and SNP primers amplified a product, of which 70% and 46%, respectively, were of the expected size. Out of verified SSR and SNP markers 84% and 82% were polymorphic. About 25% of SNPs genotyped were polymorphic in two diverse mapping populations. This study confirmed the potential of short read platforms for de novo EST assembly and identification of genetic polymorphisms in carrot. In addition we produced the first large-scale transcriptome of carrot, a species lacking genomic resources.
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影响因子：
4.4
作者：
Logacheva MD;Kasianov AS;Vinogradov DV;Samigullin TH;Gelfand MS;Makeev VJ;Penin AA
通讯作者：
Penin AA
影响因子：
4.4
作者：
Chagne, David;Gasic, Ksenija;Korban, Schuyler S.
通讯作者：
Korban, Schuyler S.
影响因子：
5.3
作者：
Dutta S;Kumawat G;Singh BP;Gupta DK;Singh S;Dogra V;Gaikwad K;Sharma TR;Raje RS;Bandhopadhya TK;Datta S;Singh MN;Bashasab F;Kulwal P;Wanjari KB;K Varshney R;Cook DR;Singh NK
通讯作者：
Singh NK
影响因子：
3.1
作者：
Cavagnaro, Pablo F.;Chung, Sang-Min;Simon, Philipp W.
通讯作者：
Simon, Philipp W.
影响因子：
1.9
作者：
Boiteux, LS;Hyman, JR;Simon, PW
通讯作者：
Simon, PW