Genomic insights into the origin, adaptive evolution and herbicide resistance of Leptochloa chinensis, a devastating tetraploid weedy grass in rice fields

第一作者：Lifeng Wang

第一单位：杂交水稻国家重点实验室

通讯作者：Lianyang Bai

 Abstarct 

背景回顾：Chinese sprangletop (Leptochloa chinensis (L.) Nees), belonging to the grass subfamily Chloridoideae, is one of the most notorious weeds in the rice ecosystems. 

千金子（Leptochloa chinensis）是禾本科虎尾草亚科千金子属的物种，是稻田系统中最为恶劣的杂草之一。

主要研究：Here we report a chromosome-scale reference genome assembly and a genomic variation map of the tetraploid L. chinensis. 

本文中，作者报道了四倍体千金子的染色体层级基因组组装以及一个基因组变异图谱。

结果1-基因组演化：The L. chinensis genome is contributed by two diploid progenitors that diverged ∼10.9 million years ago, and its two subgenomes display neither fractionation bias nor overall gene expression dominance. Comparative genomic analyses reveal substantial genome rearrangements in L. chinensis after its divergence from the common ancestor of Chloridoideae, and together with and transcriptome profiling, demonstrate the important contribution of the tetraploidization to the gene sources for the L. chinensis herbicide resistance. 

千金子基因组源自于两个已经分化了一千零九十万年的二倍体祖先种，其两个亚基因组既未表现出片段化偏性，也没有表现出整体的基因表达偏性。比较基因组显示千金子在从虎尾草亚科共同祖先分化出来后，其基因组上发生了大量的基因组重排；同时结合转录组，表明四倍化对于千金子中的除草剂抗性基因具有非常重要的贡献。

结果2-群体基因组学：Population genomic analyses of 89 accessions from China uncover that L. chinensis collected from southern/southwestern provinces have substantially higher nucleotide diversity than those from the middle and lower reaches of the Yangtze River, suggesting the spread route of L. chinensis in China from the southern/southwestern provinces to the middle and lower reaches of the Yangtze River. During this spread, L. chinensis shows significantly increased herbicide resistance, accompanied by the selection of numerous genes involved in herbicide resistance. 

通过对89份来自中国的千金子种质材料的群体基因组学分析发现，从南部/西南部省份采集的材料的核苷酸多样性显著高于长江中下游地区的材料，表明千金子是从中国的南部/西南部省份向长江中下游地区进行的传播。在传播过程中，千金子的抗除草剂性得到显著增强，同时许多与抗除草剂有关的基因被选择。

结论：Together, our study provides valuable genomic resources for the management of L. chinensisand insights into the herbicide resistance as well as the origin and adaptive evolution of L. chinensis.

综上，本文的研究为千金子的管理提供了宝贵的基因组资源，有助于深入了解千金子对除草剂的抗性以及千金子的起源和适应性演化。

** 柏连阳 **

doi: https://doi.org/10.1016/j.molp.2022.05.001

Journal: Molecular Plant

First Published: May 05, 2022

​Lifeng Wang, Xuepeng Sun, Yajun Peng, Ke Chen, Shan Wu, Yanan Guo, Jingyuan Zhang, Haona Yang, Tao Jin, Lamei Wu, Xiaomao Zhou, Bin Liang, Zhenghong Zhao, Ducai Liu, Zhangjun Fei, Lianyang Bai. (2022). Genomic insights into the origin, adaptive evolution and herbicide resistance of Leptochloa chinensis, a devastating tetraploid weedy grass in rice fields. Molecular Plant. doi: https://doi.org/10.1016/j.molp.2022.05.001.