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第一作者:Yongming Chen
第一单位:中国农业大学
通讯作者:Weilong Guo
Abstract
背景回顾:Plant genome sequencing has dramatically increased, and some species even have multiple high-quality reference versions.
提出需求:Demands for clade-specific homology inference and analysis have increased in pangenomic era. 软件开发:We proposed a novel method, GeneTribe (https://chenym1.github.io/genetribe/), for homology inference among genetically similar genomes that incorporates gene collinearity and shows better performance than traditional sequence-similarity-based methods in terms of accuracy and scalability. 示例-小麦族数据库:The Triticeae tribe is a typical allopolyploid-rich clade with complex species relationships that includes many important crops such as wheat, barley, and rye. We then built Triticeae-GeneTribe (http://wheat.cau.edu.cn/TGT/) as a homology database, by integrating 12 Triticeae genomes and 3 outgroup model genomes and implemented versatile analysis and visualization functions. 示例-科学问题1:With macrocollinearity analysis, we were able to construct a refined model illustrating the structural rearrangements of the 4A-5A-7B chromosomes in wheat as two major translocation events. 示例-科学问题2:With collinearity analysis at both the macro- and microscale, we illustrated the complex evolutionary history of homologs of the wheat vernalization gene Vrn2 as a combined result of genome translocation, duplication, and polyploidization and gene loss events. 结论:Our work provides a useful practice for connecting emerging genome assemblies, with awareness of the extensive polyploidy in plants, and will help researchers efficiently exploit genome sequence resources.
摘 要
近些年,植物全基因组测序迅猛发展,有一些植物物种甚至出现了多个高质量的参考基因组版本。因而,泛基因组研究领域亟需适用于同一进化枝特异的同源推断和分析的新方法。本文中,作者开发了一种叫做GeneTribe的方法,整合基因共线性对遗传上具有相似的基因组之间进行同源推断,并且与传统的基于序列相似性的方法相比,在准确性和可拓展性方面表现更好。小麦族(Triticeae)是一个典型的富含异源多倍体物种的进化枝,其内物种之间演化关系复杂,同时也包含了多个非常重要的作物,比如小麦、大麦和黑麦。作者利用GeneTribe构建了一个小麦族的同源数据库,整合了12个小麦族物种的基因组数据,还有3个外群的模式基因组,并且还为该在线数据库配置了多种分析功能及可视化功能。在宏观共线性分析方面,作者能够构建一个精细的模型,详细诠释了小麦中4A-5A-7B染色体的结构重排源自于两次主要的易位事件。而在宏观和微观层面的共线性分析,作者发现小麦春化基因Vrn2具有非常复杂的演化历史,综合了一系列的基因组易位、复制以及多倍化和基因丢失事件。本文为越来越多的全基因组组装之间的关联研究提供了一个非常有用的手段,有助于研究人员们更加高效的利用基因组序列资源。
通讯作者
**郭伟龙** 个人简介: 2005-2009年,北京邮电大学,学士; 2009-2014年,清华大学,博士; 2014-2016年,北京大学,博后。 研究方向: 小麦基因组学、生物信息学、表观遗传学方向。
doi: 10.1016/j.molp.2020.09.019
Journal: Molecular Plant
First Published: September 23, 2020
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