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.

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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

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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.

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