State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA; College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China.
Mol Plant. 2022 Jun 6;15(6):1045-1058. doi: 10.1016/j.molp.2022.05.001. Epub 2022 May 5.
Chinese sprangletop (Leptochloa chinensis), belonging to the grass subfamily Chloridoideae, is one of the most notorious weeds in rice ecosystems. Here, we report a chromosome-scale reference genome assembly and a genomic variation map of the tetraploid L. chinensis. The L. chinensis genome is derived from 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 transcriptome profiling, demonstrate the important contribution of tetraploidization to the gene sources for the herbicide resistance of L. chinensis. Population genomic analyses of 89 accessions from China reveal that L. chinensis accessions collected from southern/southwestern provinces have substantially higher nucleotide diversity than those from the middle and lower reaches of the Yangtze River, suggesting that L. chinensis spread in China from the southern/southwestern provinces to the middle and lower reaches of the Yangtze River. During this spread, L. chinensis developed significantly increased herbicide resistance, accompanied by the selection of numerous genes involved in herbicide resistance. Taken together, our study generated valuable genomic resources for future fundamental research and agricultural management of L. chinensis, and provides significant new insights into the herbicide resistance as well as the origin and adaptive evolution of L. chinensis.
中国看麦娘（Leptochloa chinensis），隶属于禾本科画眉草亚科，是稻田生态系统中最著名的杂草之一。在这里，我们报告了四倍体中国看麦娘的染色体水平参考基因组组装和基因组变异图谱。中国看麦娘的基因组来源于两个大约在 1090 万年前分化的二倍体祖先，其两个亚基因组既没有分化偏向，也没有整体基因表达优势。比较基因组分析揭示了中国看麦娘在与画眉草亚科的共同祖先分化后发生了大量的基因组重排，同时结合转录组分析，证明了四倍体化对中国看麦娘的除草剂抗性基因来源的重要贡献。对来自中国的 89 个样本的群体基因组分析表明，来自南部/西南部省份的中国看麦娘样本的核苷酸多样性显著高于来自长江中下游的样本，这表明中国看麦娘从南部/西南部省份向长江中下游传播。在此传播过程中，中国看麦娘的除草剂抗性显著增强，同时伴随着大量与除草剂抗性相关的基因的选择。综上所述，我们的研究为中国看麦娘的未来基础研究和农业管理提供了有价值的基因组资源，并为中国看麦娘的除草剂抗性以及起源和适应性进化提供了重要的新见解。
