Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis.
Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis.
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DOI：
10.1101/gr.139170.112
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发表时间：
2012-10
期刊：
影响因子：
7
通讯作者：
Davidson EH
中科院分区：
文献类型：
--
作者：
Tu Q;Cameron RA;Worley KC;Gibbs RA;Davidson EH
对紫球海胆10个不同的胚胎期、6个摄食期幼虫和变态期幼体以及6个成体组织的蛋白质编码RNA进行了全面的转录组分析。在这项研究中，我们汇集了来自所有这些来源的转录组，并专注于它们为这个最近测序的模型系统的基因组中的基因结构提供的见解。基因组最初是通过使用计算基因模型预测算法来注释的。当将读段映射到基因组并适当过滤和分析时，在转录组中回收了大部分这些预测的基因。然而，在一个人工策划的子集中，我们发现超过一半的计算基因模型预测是不完美的，包含错误，如缺失外显子，预测不存在的外显子，错误的内含子/外显子边界，相邻基因的融合，以及从单个基因预测多个基因。转录组数据已被用于提供整个基因组的基因模型预测的系统升级，极大地提高了基因组序列的研究可用性。我们已经构建了新的公共数据库，其中包含来自转录组分析的信息。基于转录本的基因模型数据用于定义S. purpuratus蛋白编码基因。此外，我们还构建了一个自定义的海胆基因本体，并将大约7000个不同的注释转录本分配到24个功能类。强相关性变得明显给定的功能本体类和结构特性，包括基因大小，外显子数量，外显子和内含子的大小之间。
A comprehensive transcriptome analysis has been performed on protein-coding RNAs of Strongylocentrotus purpuratus, including 10 different embryonic stages, six feeding larval and metamorphosed juvenile stages, and six adult tissues. In this study, we pooled the transcriptomes from all of these sources and focused on the insights they provide for gene structure in the genome of this recently sequenced model system. The genome had initially been annotated by use of computational gene model prediction algorithms. A large fraction of these predicted genes were recovered in the transcriptome when the reads were mapped to the genome and appropriately filtered and analyzed. However, in a manually curated subset, we discovered that more than half the computational gene model predictions were imperfect, containing errors such as missing exons, prediction of nonexistent exons, erroneous intron/exon boundaries, fusion of adjacent genes, and prediction of multiple genes from single genes. The transcriptome data have been used to provide a systematic upgrade of the gene model predictions throughout the genome, very greatly improving the research usability of the genomic sequence. We have constructed new public databases that incorporate information from the transcriptome analyses. The transcript-based gene model data were used to define average structural parameters for S. purpuratus protein-coding genes. In addition, we constructed a custom sea urchin gene ontology, and assigned about 7000 different annotated transcripts to 24 functional classes. Strong correlations became evident between given functional ontology classes and structural properties, including gene size, exon number, and exon and intron size.
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影响因子：
14.9
作者：
Cameron RA;Samanta M;Yuan A;He D;Davidson E
通讯作者：
Davidson E
影响因子：
2.7
作者：
Livi, Carolina B.;Davidson, Enic H.
通讯作者：
Davidson, Enic H.
DOI：
10.1073/pnas.0711220105
发表时间：
2008-04-22
影响因子：
11.1
作者：
Oliveri, Paola;Tu, Qiang;Davidson, Eric H.
通讯作者：
Davidson, Eric H.
影响因子：
5.8
作者：
Huang, Ying;Niu, Beifang;Li, Weizhong
通讯作者：
Li, Weizhong
影响因子：
2.7
作者：
Otim, O;Amore, G;Davidson, EH
通讯作者：
Davidson, EH