Functional annotation of 19,841 Populus nigra full-length enriched cDNA clones
Functional annotation of 19,841 Populus nigra full-length enriched cDNA clones
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DOI：
10.1186/1471-2164-8-448
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发表时间：
2007-12-03
期刊：
影响因子：
4.4
通讯作者：
Shinohara, Kenji
中科院分区：
文献类型：
--
作者：
Nanjo, Tokihiko;Sakurai, Tetsuya;Shinohara, Kenji
背景：杨树基因组小，是理想的模式植物之一。杨树的结构基因组学已经达到了一个断点，整个基因组的核苷酸已经确定。进入后基因组时代，杨树功能基因组学对植物科学的全面发展具有重要意义。服务于功能基因组学的生物资源开发正在迅速发展。近年来，人们在各种植物物种中积累了表达序列标签（est），从而加快了基因的功能分析。来自全长cDNA克隆的ESTs对于精确的分子注释尤其有效。我们促进了杨树全长富集cDNA克隆ESTs的收集和注释，作为该树种功能基因组学的一部分。结果：多年来，我们一直在收集母杨（Populus nigra var. italica）的全长富集cDNA。通过对黑鲈全长（PnFL） cDNA文库的测序，我们得到了116000个5′端或3′端ESTs，对应于19841个非冗余PnFL克隆。PnFL cDNA克隆群体占杨树基因组预测基因的44%。结论：我们的黑桫椤全长富集克隆资源有望为进一步深入了解杨树基因组注释和功能基因组学提供有价值的工具。
Background: Populus is one of favorable model plants because of its small genome. Structural genomics of Populus has reached a breakpoint as nucleotides of the entire genome have been determined. Reaching the post genome era, functional genomics of Populus is getting more important for well-comprehended plant science. Development of bioresorce serving functional genomics is making rapid progress. Huge efforts have achieved deposits of expressed sequence tags (ESTs) in various plant species consequently accelerating functional analysis of genes. ESTs from full-length cDNA clones are especially powerful for accurate molecular annotation. We promoted collection and annotation of the ESTs from Populus full-length enriched cDNA clones as part of functional genomics of tree species.Results: We have been collecting the full-length enriched cDNA of the female poplar (Populus nigra var. italica) for years. By sequencing P. nigra full-length (PnFL) cDNA libraries, we generated about 116,000 5'- end or 3'-end ESTs corresponding to 19,841 nonredundant PnFL clones. Population of PnFL cDNA clones represents 44% of the predicted genes in the Populus genome.Conclusion: Our resource of P. nigra full-length enriched clones is expected to provide valuable tools to gain further insight into genome annotation and functional genomics in Populus.