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Nature Plants:高质量芸薹属植物黑芥基因组

已有 2130 次阅读 2020-8-12 09:33 |个人分类:每日摘要|系统分类:论文交流

A high-contiguity Brassica nigra genome localizes active centromeres and defines the ancestral Brassica genome

第一作者Sampath Perumal

第一单位加拿大农业及农业食品部

通讯作者Isobel A. P. Parkin


 Abstract 


背景回顾It is only recently, with the advent of long-read sequencing technologies, that we are beginning to uncover previously uncharted regions of complex and inherently recursive plant genomes. 


主要研究:To comprehensively study and exploit the genome of the neglected oilseed Brassica nigra, we generated two high-quality nanopore de novo genome assemblies.


结果-组装结果:The N50 contig lengths for the two assemblies were 17.1 Mb (12  contigs), one of the best among 324  sequenced plant genomes, and 0.29 Mb (424  contigs), respectively, reflecting recent improvements in the technology.


结果-质量评估:Comparison with a de novo short-read assembly corroborated genome integrity and quantified sequence-related error rates (0.2%). The contiguity and coverage allowed unprecedented access to low-complexity regions of the genome. 


结果-着丝粒特征:Pericentromeric regions and coincidence of hypomethylation enabled localization of active centromeres and identified centromere-associated ALE family retro-elements that appear to have proliferated through relatively recent nested transposition events (<1 Ma).


结果-祖先基因组预测Genomic distances calculated based on synteny relationships were used to define a post-triplication Brassica-specific ancestral genome, and to calculate the extensive rearrangements that define the evolutionary distance separating B. nigra from its diploid relatives.


 摘  要 


直到最近,随着长read测序技术的出现,我们开始探索之前植物基因组上较为复杂的神秘陌生区域。为全面研究和开发被忽视的芸薹属植物黑芥的基因组,作者在本文中报道了两个由纳米孔测序、组装的高质量基因组参考序列。这两个组装版本的contig N50分别为17.1Mb(12个contigs)和0.29Mb(424个contigs),前一个组装质量属于目前已报道的324个已测序基因组中质量最好的梯队,反应了测序技术进步对于组装质量提升的作用。通过与一个基于短read测序组装的基因组比较,再一次证实了该版本组装的连续性较好,并且估算序列错误率约为0.2%。作者这里报道的基因组组装在连续性以及覆盖度上的提升有助于对于基因组低复杂区域的详细解析。着丝粒区域和低甲基化的特征帮助作者鉴定到了活跃着丝粒在基因组上的位置,并且还鉴定到了着丝粒相关ALE家族逆转录元件似乎通过近期的嵌套转座事件进行了扩张。基于共线性区域的基因组遗传距离计算被用于定义三倍化后芸薹属物种特异性的祖先基因组序列,并且基于此计算了黑芥与其二倍体近缘种分化之后产生的广泛基因组重排,从而确定二者之间的演化距离。


 通讯作者 


**Isobel A. P. Parkin**


研究方向:

芸苔属植物基因组学、比较基因组、基因表达分析以及非生物胁迫响应。


doi: 10.1038/s41477-020-0735-y


Journal: Nature Plants

Published date: August 10, 2020



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