A global assembly of cotton ESTs
A global assembly of cotton ESTs
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DOI：
10.1101/gr.4602906
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发表时间：
2006-03-01
期刊：
影响因子：
7
通讯作者：
Wendel, JF
中科院分区：
文献类型：
--
作者：
Udall, JA;Swanson, JM;Wendel, JF
从30个cDNA文库中收集了大约185,000个包含> 94,800,000个核苷酸的棉属EST序列，这些文库是在一系列条件下（包括干旱胁迫和病原体挑战）从多种组织和器官构建的。这些文库源自异源多倍体棉花（陆地棉；A(T) 和 D-T 基因组）及其两个二倍体祖细胞，树木棉（A 基因组）和雷蒙德棉（D 基因组）。使用 EST 组装和查看程序 (PAVE) 组装 EST，产生 22,030 个重叠群和 29,077 个单基因（51,107 个单基因）。单例和重叠群之间的进一步比较导致识别出 33,665 个示例序列，这些序列代表一组非冗余的推定棉基因，包含部分或全长编码区以及通常一个或两个 UTR。该装配体及其 UniProt BLASTX 命中、GO 注释和 Pfam 分析结果可作为棉花基因组学的公共资源免费获取。由于来自二倍体和异源四倍体棉花的 EST 组合在一个组件中，因此在许多情况下，我们能够通过生物信息学方法区分异源四倍体棉花中的重复基因，并将它们分配给 A 或 D 基因组。组装和相关信息为未来棉花功能和进化基因组学的研究提供了框架。
Approximately 185,000 Gossypium EST sequences comprising > 94,800,000 nucleotides were amassed from 30 cDNA libraries constructed from a variety Of tissues and organs under a range of conditions, including drought stress and pathogen challenges. These libraries were derived from allopolyploid cotton (Gossypium hirsutum; A(T) and D-T genomes) as well as its two diploid progenitors, Gossypium arboreum (A genome) and Gossypium raimondii (D genome). ESTs were assembled using the Program for Assembling and Viewing ESTs (PAVE), resulting in 22,030 contigs and 29,077 singletons (51,107 unigenes). Further comparisons among the singletons and contigs led to recognition of 33,665 exemplar sequences that represent a nonredundant set of putative Gossypium genes containing partial or full-length coding regions and usually one or two UTRs. The assembly, along with their UniProt BLASTX hits, GO annotation, and Pfam analysis results, are freely accessible as a public resource for cotton genomics. Because ESTs from diploid and allotetraploid Gossypium were combined in a single assembly, we were in many cases able to bioinformatically distinguish duplicated genes in allotetraploid cotton and assign them to either the A or D genome. The assembly and associated information provide a framework for future investigation of cotton functional and evolutionary genomics.