Comparative Genome Analyses Highlight Transposon-Mediated Genome Expansion and the Evolutionary Architecture of 3D Genomic Folding in Cotton

文献类型： 外文期刊

第一作者： Wang, Maojun

作者： Wang, Maojun;Li, Jianying;Wang, Pengcheng;Liu, Zhenping;Zhao, Guannan;Xu, Zhongping;Pei, Liuling;Zhang, Xianlong;Liu, Fang;Wang, Kunbo;Grover, Corrinne E.;Wendel, Jonathan F.

作者机构：

关键词： Gossypium; genome expansion; transposable element; chromatin compartment; TAD reorganization; 3D genome architecture

期刊名称：MOLECULAR BIOLOGY AND EVOLUTION （ 影响因子：16.24； 五年影响因子：18.67 ）

ISSN： 0737-4038

年卷期： 2021 年 38 卷 9 期

页码：

收录情况： SCI

摘要： Transposable element (TE) amplification has been recognized as a driving force mediating genome size expansion and evolution, but the consequences for shaping 3D genomic architecture remains largely unknown in plants. Here, we report reference-grade genome assemblies for three species of cotton ranging 3-fold in genome size, namely Gossypium rotundifolium (K-2), G. arboreum (A(2)), and G. raimondii (D-5), using Oxford Nanopore Technologies. Comparative genome analyses document the details of lineage-specific TE amplification contributing to the large genome size differences (K-2, 2.44 Gb; A(2), 1.62 Gb; D-5, 750.19 Mb) and indicate relatively conserved gene content and synteny relationships among genomes. We found that approximately 17% of syntenic genes exhibit chromatin status change between active ("A") and inactive ("B") compartments, and TE amplification was associated with the increase of the proportion of A compartment in gene regions (similar to 7,000 genes) in K-2 and A(2) relative to D-5. Only 42% of topologically associating domain (TAD) boundaries were conserved among the three genomes. Our data implicate recent amplification of TEs following the formation of lineage-specific TAD boundaries. This study sheds light on the role of transposon-mediated genome expansion in the evolution of higher-order chromatin structure in plants.

分类号：

  • 相关文献
作者其他论文 更多>>
  • Health assessment based on exposure to microplastics in tropical agricultural soil

    作者：Lin, Bigui;Wang, Luya;Liu, Beibei;Liu, Fang;Wu, Lin;Wei, Chaoxian;Lin, Bigui;Wang, Luya;Liu, Beibei;Wu, Lin;Wei, Chaoxian;Lin, Bigui;Wang, Luya;Liu, Beibei;Wu, Lin;Wei, Chaoxian;Chen, Qiyu;Liu, Zhilei;Chen, Xichao;Zhang, Zongyao;Wen, Shaobai;Liu, Fang

    关键词：Microplastics; Agricultural soil; Size distribution analysis; Dimensionality of MPs; Health exposure assessment

  • Widespread incomplete lineage sorting and introgression shaped adaptive radiation in the Gossypium genus

    作者：Xu, Yanchao;Zhou, Zhongli;Cai, Xiaoyan;Umer, Muhammad Jawad;Hou, Yuqing;Wang, Yuhong;Wang, Kunbo;Yu, Shuxun;Liu, Fang;Xu, Yanchao;Wei, Yangyang;Liu, Yuling;Peng, Renhai;Xu, Yanchao;Cai, Xiaoyan;Boden, Scott A.;Safdar, Luqman B.;Jin, Dingsha;Wall, Sarah Brooke;Zhang, Baohong;Liu, Fang

    关键词：cotton speciation; Gossypium genus; incomplete lineage sorting; ILS; phylogenetic analysis; gene tree resolution

  • MCSS: microbial community simulator based on structure

    作者：Hui, Xingqi;Liu, Fang;Hui, Xingqi;Yang, Jinbao;Pan, Weihua;Yang, Jinbao;Sun, Jinhuan;Liu, Fang

    关键词：metagenome; microbiome communities; long reads; simulator; assembly

  • Linkage and association mapping in multi-parental populations reveal the genetic basis of carotenoid variation in maize kernels

    作者：Yin, Pengfei;Fu, Xiuyi;Feng, Haiying;Yang, Yanyan;Xu, Jing;Zhang, Xuan;Wang, Min;Ji, Shenghui;Zhao, Binghao;Fang, Hui;Du, Xiaoxia;Li, Yaru;Hu, Shuting;Li, Kun;Xu, Shutu;Li, Zhigang;Li, Jiansheng;Yang, Xiaohong;Yin, Pengfei;Fu, Xiuyi;Feng, Haiying;Yang, Yanyan;Xu, Jing;Zhang, Xuan;Wang, Min;Ji, Shenghui;Zhao, Binghao;Fang, Hui;Du, Xiaoxia;Li, Yaru;Hu, Shuting;Li, Kun;Xu, Shutu;Li, Zhigang;Li, Jiansheng;Yang, Xiaohong;Fu, Xiuyi;Wang, Yuandong;Liu, Fang;Li, Jiansheng;Yang, Xiaohong;Xiao, Yingni;Yang, Xiaohong

    关键词：Carotenoids; Linkage analysis; Association mapping; Plastid terminal oxidase

  • Using rice straw-augmented ecological floating beds to enhance nitrogen removal in carbon-limited wastewater

    作者：Cai, Xixi;Li, Jianying;Wu, Haoping;Yang, Siyu;You, Yi;Zou, Chunping;Qin, Hongjie;Cai, Xixi;Li, Jianying;Wu, Haoping;Yang, Siyu;You, Yi;Zou, Chunping;Qin, Hongjie;Li, Dunhai;Xing, Wei;Guo, Xiaoyu;Li, Jibing;Li, Jibing

    关键词：Microbial community; Denitrification; Low -carbon sewage; Aquatic macrophytes

  • Genetic Analysis of Cotton Fiber Traits in Gossypium Hybrid Lines

    作者：Wang, Heng;Cai, Xiaoyan;Umer, Muhammad Jawad;Xu, Yanchao;Hou, Yuqing;Zheng, Jie;Liu, Fang;Wang, Kunbo;Zhou, Zhongli;Chen, Mengshan;Ma, Shuping;Yu, Jingzhong;Cai, Xiaoyan;Zheng, Jie;Liu, Fang;Liu, Fang;Cai, Xiaoyan;Hou, Yuqing;Zheng, Jie;Liu, Fang

    关键词：

  • Transcriptional landscape of cotton roots in response to salt stress at single-cell resolution

    作者：Li, Pengtao;Liu, Qiankun;Wei, Yangyang;Liu, Yuling;Lu, Quanwei;Hu, Nan;Wang, Tao;Cheng, Shuang;Li, Zhaoguo;Zhao, Zilin;Li, Yanfang;Peng, Renhai;Li, Pengtao;Liu, Qiankun;Xing, Chaozhu;Han, Jiangping;Cai, Xiaoyan;Zhou, Zhongli;Wang, Kunbo;Liu, Fang;Li, Pengtao;Xing, Chaozhu;Liu, Fang;Peng, Renhai;Liu, Qiankun;Cheng, Shuang;Li, Zhaoguo;Peng, Renhai;Xu, Zhongping;Zhu, Xiangqian;Jin, Shuangxia;Ding, Fang;Zhang, Baohong

    关键词：cotton; salt stress; scRNA-seq; root cell types; virus-induced gene silencing

微信小程序