Cotton D genome assemblies built with long-read data unveil mechanisms of centromere evolution and stress tolerance divergence

BMC Biology

Fuyan Liu¹  Weinan Li²  Shaoliang Peng³  Lisen Liu⁴  Yanli Chen⁴  Wei Hu⁴  Yuying Jin⁴  Zhaoen Yang⁵  Fuguang Li⁵  Xiaoyang Ge⁵ 

[1] Biomarker Technologies Corporation, 101300, Beijing, China;College of Computer Science and Electronic Engineering, Hunan University, 410082, Changsha, China;College of Computer Science and Electronic Engineering, Hunan University, 410082, Changsha, China;School of Computer Science, National University of Defense Technology, 410073, Changsha, China;Peng Cheng Lab, 518000, Shenzhen, China;Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000, Anyang, China;Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001, Zhengzhou, China;Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000, Anyang, China;

关键词: G. thurberi;    G. davidsonii;    Salt tolerance;    Verticillium wilt;    Structural variation;    Long-range interactions;    Hi-C;    3D genome;    Gossypium;   

DOI  :  10.1186/s12915-021-01041-0

来源: Springer

【 摘 要 】

BackgroundMany of genome features which could help unravel the often complex post-speciation evolution of closely related species are obscured because of their location in chromosomal regions difficult to accurately characterize using standard genome analysis methods, including centromeres and repeat regions.ResultsHere, we analyze the genome evolution and diversification of two recently diverged sister cotton species based on nanopore long-read sequence assemblies and Hi-C 3D genome data. Although D genomes are conserved in gene content, they have diversified in gene order, gene structure, gene family diversification, 3D chromatin structure, long-range regulation, and stress-related traits. Inversions predominate among D genome rearrangements. Our results support roles for 5mC and 6mA in gene activation, and 3D chromatin analysis showed that diversification in proximal-vs-distal regulatory-region interactions shape the regulation of defense-related-gene expression. Using a newly developed method, we accurately positioned cotton centromeres and found that these regions have undergone obviously more rapid evolution relative to chromosome arms. We also discovered a cotton-specific LTR class that clarifies evolutionary trajectories among diverse cotton species and identified genetic networks underlying the Verticillium tolerance of Gossypium thurberi (e.g., SA signaling) and salt-stress tolerance of Gossypium davidsonii (e.g., ethylene biosynthesis). Finally, overexpression of G. thurberi genes in upland cotton demonstrated how wild cottons can be exploited for crop improvement.ConclusionsOur study substantially deepens understanding about how centromeres have developed and evolutionarily impacted the divergence among closely related cotton species and reveals genes and 3D genome structures which can guide basic investigations and applied efforts to improve crops.

【 授权许可】

CC BY