Maojun Wang, Jianying Li, Zhengyang Qi, Yuexuan Long, Liuling Pei, Xianhui Huang, Corrinne E. Grover, Xiongming Du, Chunjiao Xia, Pengcheng Wang, Zhenping Liu, Jiaqi You, Xuehan Tian, Yizan Ma, Ruipeng Wang, Xinyuan Chen, Xin He, David D. Fang, Yuqiang Sun, Lili Tu, Shuangxia Jin, Longfu Zhu, Jonathan F. Wendel, Xianlong Zhang
Nature Genetics(2022), Published: 06 December 2022
Phenotypic diversity and evolutionary innovation ultimately trace to variation in genomic sequence and rewiring of regulatory networks. Here, we constructed a pan-genome of theGossypiumgenus using ten representative diploid genomes. We document the genomic evolutionary history and the impact of lineage-specific transposon amplification on differential genome composition. The pan-3D genome reveals evolutionary connections between transposon-driven genome size variation and both higher-order chromatin structure reorganization and the rewiring of chromatin interactome. We linked changes in chromatin structures to phenotypic differences in cotton fiber and identified regulatory variations that decode the genetic basis of fiber length, the latter enabled by sequencing 1,005 transcriptomes during fiber development. We showcase how pan-genomic, pan-3D genomic and genetic regulatory data serve as a resource for delineating the evolutionary basis of spinnable cotton fiber. Our work provides insights into the evolution of genome organization and regulation and will inform cotton improvement by enabling regulome-based approaches.