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第一作者:Fabricio B. Machado
第一单位:巴西北弗卢米嫩塞州立大学
通讯作者:Thiago M. Venancio
Abstract
背景1-大豆很重要:Soybean (Glycine max [L.] Merr.) is a major crop in animal feed and human nutrition, mainly for its rich protein and oil contents.
背景2-大豆数据很多:The remarkable rise in soybean transcriptome studies over the past 5 years generated an enormous amount of RNA‐seq data, encompassing various tissues, developmental conditions and genotypes. 主要研究:In this study, we have collected data from 1298 publicly available soybean transcriptome samples, processed the raw sequencing reads and mapped them to the soybean reference genome in a systematic fashion. 结果1-基因表达:We found that 94% of the annotated genes (52 737/56 044) had detectable expression in at least one sample. Unsupervised clustering revealed three major groups, comprising samples from aerial, underground and seed/seed‐related parts. 结果2-看家基因与偏性表达:We found 452 genes with uniform and constant expression levels, supporting their roles as housekeeping genes. On the other hand, 1349 genes showed heavily biased expression patterns towards particular tissues. 结果3-可变剪切:A transcript‐level analysis revealed that 95% (70 963 of 74 490) of the assembled transcripts have intron chains exactly matching those from known transcripts, whereas 3256 assembled transcripts represent potentially novel splicing isoforms. 结果4-在线数据库:The dataset compiled here constitute a new resource for the community, which can be downloaded or accessed through a user‐friendly web interface at http://venanciogroup.uenf.br/resources/. 结论:This comprehensive transcriptome atlas will likely accelerate research on soybean genetics and genomics.
摘 要
大豆由于其含有丰富的蛋白与籽油,在动物饲料与人类营养领域都是主要的作物。过去的5年中,对于大豆的转录组研究产生了海量的RNA-seq数据,包括多个组织、发育条件以及基因型。本文中,作者收集了1298份公共发表的大豆转录组数据,以批量系统的方式进行原始数据处理以及大豆参考基因组比对工作。作者发现大豆基因组中56044个注释的基因中,52737个基因至少在一个样本中存在表达。非监督聚类(Unsupervised clustering)分析显示这些样本可以聚成三个群体,分别包含来自地上部分组织,地下部分组织与种子及种子相关部分组织。作者发现452个基因存在相当且恒定的表达水平,说明其作为看家基因发挥作用。另外,1349个基因在特定的组织中存在非常严重的偏性表达模式。转录本水平的分析显示,95%的组装转录本具有与已知转录本一致的内含子链,但也鉴定了3256个转录本作为新的剪切形式存在。本文所报道的数据均可以在可交互网站http://venanciogroup.uenf.br/resources/中在线查询。本研究所提供的综合转录本图谱将有助于加速大豆遗传学与基因组学的深入研究。
通讯作者
**Thiago M. Venancio** 个人简介: 2004-2008年,巴西圣保罗大学,博士; 2008-2010年,美国NCBI-NIH,博后。 研究方向: 演化如何塑造基因组与生物网络。
doi: 10.1111/tpj.14850
Journal: the plant journal
Published date: Augus 13, 2020
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