Araport11: a complete reannotation of the Arabidopsis thaliana reference genome
Araport11: a complete reannotation of the Arabidopsis thaliana reference genome
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DOI：
10.1111/tpj.13415
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发表时间：
2017-02-01
期刊：
影响因子：
7.2
通讯作者：
Town, Christopher D.
中科院分区：
文献类型：
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作者：
Cheng, Chia-Yi;Krishnakumar, Vivek;Town, Christopher D.
开花植物拟南芥（Arabidopsis thaliana）是植物生物学许多方面研究的双子叶模式生物。对其基因组的全面注释为理解所有类型的转录本的功能和活性铺平了道路，包括mRNA、各种非编码RNA和小RNA。TAIR 10注释更新对拟南芥研究产生了深远的影响，但在50多年前发布。保持注释的准确性仍然是今后取得进展的先决条件。使用整合注释管道，我们从113个数据集组装了组织特异性RNA-Seq文库，并在11个组织中构建了48359个蛋白质编码基因的转录模型。此外，我们使用已发表的数据集和内部分析结果注释了各种类型的非编码RNA，包括microRNA、长基因间RNA、小核仁RNA、天然反义转录物、小核RNA和小RNA。总之，我们确定了635个新的蛋白质编码基因，508个新的转录区，5178个非编码RNA，和35846个小RNA位点，以前未注释。对剪接事件和基于RNA-Seq的表达谱的分析揭示了基因结构、非翻译区和剪接活动的景观比以前认识到的更复杂。此外，我们提出了692个均匀表达的管家基因，其中43%的人类直系同源物也是管家基因。这种更新的拟南芥基因组注释与基因模型的分辨率大幅提高，不仅将进一步我们了解这种植物模型的生物学过程，也对其他物种。
The flowering plant Arabidopsis thaliana is a dicot model organism for research in many aspects of plant biology. A comprehensive annotation of its genome paves the way for understanding the functions and activities of all types of transcripts, including mRNA, the various classes of non-coding RNA, and small RNA. The TAIR10 annotation update had a profound impact on Arabidopsis research but was released more than 5years ago. Maintaining the accuracy of the annotation continues to be a prerequisite for future progress. Using an integrative annotation pipeline, we assembled tissue-specific RNA-Seq libraries from 113 datasets and constructed 48359 transcript models of protein-coding genes in eleven tissues. In addition, we annotated various classes of non-coding RNA including microRNA, long intergenic RNA, small nucleolar RNA, natural antisense transcript, small nuclear RNA, and small RNA using published datasets and in-house analytic results. Altogether, we identified 635 novel protein-coding genes, 508 novel transcribed regions, 5178 non-coding RNAs, and 35846 small RNA loci that were formerly unannotated. Analysis of the splicing events and RNA-Seq based expression profiles revealed the landscapes of gene structures, untranslated regions, and splicing activities to be more intricate than previously appreciated. Furthermore, we present 692 uniformly expressed housekeeping genes, 43% of whose human orthologs are also housekeeping genes. This updated Arabidopsis genome annotation with a substantially increased resolution of gene models will not only further our understanding of the biological processes of this plant model but also of other species.