A complete gap-free diploid genome in Saccharum complex and the genomic footprints of evolution in the highly polyploid Saccharum genus

文献类型： 外文期刊

第一作者： Wang, Tianyou

作者： Wang, Tianyou;Qi, Yiying;Wang, Yuhao;Wang, Yongjun;Pan, Haoran;Li, Zhen;Deng, Zuhu;Wang, Baiyu;Hua, Xiuting;Gao, Ruiting;Yu, Zehuai;Li, Yihan;Chen, Baoshan;Zhang, Muqing;Yao, Wei;Zhang, Jisen;Wang, Baiyu;Hua, Xiuting;Gao, Ruiting;Yu, Zehuai;Li, Yihan;Chen, Baoshan;Zhang, Muqing;Yao, Wei;Zhang, Jisen;Tang, Haibao;Zhang, Qing;Zhang, Zhe;Mei, Jing;Zhang, Yixing;Meng, Xue;Chen, Shuqi;Shi, Huihong;Ming, Ray;Zhang, Zeyu;Gu, Lianfeng;Wang, Gang;Huang, Yongji;Liu, Xinlong;Wang, Jianping

作者机构：

期刊名称：NATURE PLANTS （ 影响因子：18.0； 五年影响因子：18.6 ）

ISSN： 2055-026X

年卷期： 2023 年 9 卷 4 期

页码：

收录情况： SCI

摘要： The sugarcane relative, Erianthus rufipilus, is one of the rare diploid species within the Saccharum complex. Its gap-free genome reveals centromere diversification, epigenetics of a palaeo-duplicated chromosome and evolution of Saccharum. A diploid genome in the Saccharum complex facilitates our understanding of evolution in the highly polyploid Saccharum genus. Here we have generated a complete, gap-free genome assembly of Erianthus rufipilus, a diploid species within the Saccharum complex. The complete assembly revealed that centromere satellite homogenization was accompanied by the insertions of Gypsy retrotransposons, which drove centromere diversification. An overall low rate of gene transcription was observed in the palaeo-duplicated chromosome EruChr05 similar to other grasses, which might be regulated by methylation patterns mediated by homologous 24 nt small RNAs, and potentially mediating the functions of many nucleotide-binding site genes. Sequencing data for 211 accessions in the Saccharum complex indicated that Saccharum probably originated in the trans-Himalayan region from a diploid ancestor (x = 10) around 1.9-2.5 million years ago. Our study provides new insights into the origin and evolution of Saccharum and accelerates translational research in cereal genetics and genomics.

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