Tissue resolved, gene structure refined equine transcriptome.
Tissue resolved, gene structure refined equine transcriptome.
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组织分辨的基因结构完善了马转录组。
DOI：
10.1186/s12864-016-3451-2
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发表时间：
2017-01-20
期刊：
影响因子：
4.4
通讯作者：
Brown CT
中科院分区：
文献类型：
--
作者：
Mansour TA;Scott EY;Finno CJ;Bellone RR;Mienaltowski MJ;Penedo MC;Ross PJ;Valberg SJ;Murray JD;Brown CT
转录组解释依赖于高质量的参考转录组来准确量化基因表达以及遗传变异的功能分析。目前的马基因组注释缺乏评估基因表达（尤其是亚型水平）所需的特异性和敏感性，并且对非翻译区（UTR）使用的注释不足。我们为马构建了一个注释管道，并使用它将来自多个 RNA-seq 数据集的 19 亿条读数整合到一个新的精炼转录组中。该马转录组整合了 59 个个体的 8 个不同组织，改善了基因结构和亚型分辨率，同时提供了大量的组织特异性信息。我们在管道中使用了四个级别的转录物过滤，旨在产生适合不同下游分析的多个转录组版本。我们最精细的转录组包括 36,876 个基因和 76,125 个亚型，其中 6474 个候选转录位点对于马转录组来说是新颖的。我们采用了各种描述性统计数据和数字来证明转录组的质量和内容。该管道提供的马转录组显示了迄今为止任何马转录组的最佳组织特异性分辨率，并且对于多种下游分析来说是灵活的。我们鼓励将更多的马转录组与我们的注释管道整合，以继续和改进马转录组。本文的在线版本 (doi:10.1186/s12864-016-3451-2) 包含补充材料，可供授权用户使用。
Transcriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the horse genome lacks the specificity and sensitivity necessary to assess gene expression especially at the isoform level, and suffers from insufficient annotation of untranslated regions (UTR) usage. We built an annotation pipeline for horse and used it to integrate 1.9 billion reads from multiple RNA-seq data sets into a new refined transcriptome. This equine transcriptome integrates eight different tissues from 59 individuals and improves gene structure and isoform resolution, while providing considerable tissue-specific information. We utilized four levels of transcript filtration in our pipeline, aimed at producing several transcriptome versions that are suitable for different downstream analyses. Our most refined transcriptome includes 36,876 genes and 76,125 isoforms, with 6474 candidate transcriptional loci novel to the equine transcriptome. We have employed a variety of descriptive statistics and figures that demonstrate the quality and content of the transcriptome. The equine transcriptomes that are provided by this pipeline show the best tissue-specific resolution of any equine transcriptome to date and are flexible for several downstream analyses. We encourage the integration of further equine transcriptomes with our annotation pipeline to continue and improve the equine transcriptome. The online version of this article (doi:10.1186/s12864-016-3451-2) contains supplementary material, which is available to authorized users.