Efficient plant gene identification based on interspecies mapping of full-length cDNAs.
Efficient plant gene identification based on interspecies mapping of full-length cDNAs.
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DOI：
10.1093/dnares/dsq017
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发表时间：
2010-10
期刊：
影响因子：
--
通讯作者：
Itoh T
中科院分区：
文献类型：
--
作者：
Amano N;Tanaka T;Numa H;Sakai H;Itoh T
我们提出了一个基于全长cdna （flcdna）准确预测外显子-内含子结构和蛋白质编码序列（CDSs）的注释管道。该标注管道用于鉴定10种植物基因组中的基因。特别是，我们表明FLcDNA在物种间的基因组定位对于充分利用FLcDNA资源具有重要价值，这些资源的可用性仅限于几个物种。由于不同物种间flcdna的5′和3′端较低的序列保守性往往导致CDSs被截断，我们开发了一种改进的算法，通过截断的CDSs两端的延伸来识别完整的CDSs。将7801个单子叶flcdna定位到水稻基因组中，检测到22 142个蛋白质编码区。此外，在比较两个映射程序和三个从头开始预测程序时，我们发现我们的管道更能识别完整的cds。正如单子叶种间定位所证明的那样，flcdna与基因组之间的核苷酸一致性约为80%，由此推断的CDSs足够准确。最后，我们对10个单子叶和双子叶的基因组进行了种间和种内定位，并鉴定了210 551个位点的基因。flcdna的种间定位有望有效预测新测序基因组中的基因和CDSs。
We present an annotation pipeline that accurately predicts exon–intron structures and protein-coding sequences (CDSs) on the basis of full-length cDNAs (FLcDNAs). This annotation pipeline was used to identify genes in 10 plant genomes. In particular, we show that interspecies mapping of FLcDNAs to genomes is of great value in fully utilizing FLcDNA resources whose availability is limited to several species. Because low sequence conservation at 5′- and 3′-ends of FLcDNAs between different species tends to result in truncated CDSs, we developed an improved algorithm to identify complete CDSs by the extension of both ends of truncated CDSs. Interspecies mapping of 71 801 monocot FLcDNAs to the Oryza sativa genome led to the detection of 22 142 protein-coding regions. Moreover, in comparing two mapping programs and three ab initio prediction programs, we found that our pipeline was more capable of identifying complete CDSs. As demonstrated by monocot interspecies mapping, in which nucleotide identity between FLcDNAs and the genome was ∼80%, the resultant inferred CDSs were sufficiently accurate. Finally, we applied both inter- and intraspecies mapping to 10 monocot and dicot genomes and identified genes in 210 551 loci. Interspecies mapping of FLcDNAs is expected to effectively predict genes and CDSs in newly sequenced genomes.
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影响因子：
14.9
作者：
UniProt Consortium
通讯作者：
UniProt Consortium
影响因子：
3
作者：
Majoros WH;Pertea M;Delcher AL;Salzberg SL
通讯作者：
Salzberg SL
影响因子：
14.9
作者：
Ouyang S;Zhu W;Hamilton J;Lin H;Campbell M;Childs K;Thibaud-Nissen F;Malek RL;Lee Y;Zheng L;Orvis J;Haas B;Wortman J;Buell CR
通讯作者：
Buell CR
影响因子：
64.8
作者：
Matsumoto, T;Wu, JZ;Sugiura, M
通讯作者：
Sugiura, M
DOI：
10.1093/dnares/dsn018
发表时间：
2008-10
期刊：
DNA research : an international journal for rapid publication of reports on genes and genomes
影响因子：
--
作者：
Lu T;Yu S;Fan D;Mu J;Shangguan Y;Wang Z;Minobe Y;Lin Z;Han B
通讯作者：
Han B