Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer

Yuan Yin, Huizhong Fan, Botong Zhou, Yibo Hu, Guangyi Fan, Jinhuan Wang, Fan Zhou, Wenhui Nie, Chenzhou Zhang, Lin Liu, Zhenyu Zhong, Wenbo Zhu, Guichun Liu, Zeshan Lin, Chang Liu, Jiong Zhou, Guangping Huang, Zihe Li, Jianping Yu, Yaolei Zhang, Yue Yang, Bingzhao Zhuo, Baowei Zhang, Jiang Chang, Haiyuan Qian, Yingmei Peng, Xianqing Chen, Lei Chen, Zhipeng Li, Qi Zhou (), Wen Wang () and Fuwen Wei ()
Additional contact information
Yuan Yin: Northwestern Polytechnical University
Huizhong Fan: Institute of Zoology, Chinese Academy of Sciences
Botong Zhou: Northwestern Polytechnical University
Yibo Hu: Institute of Zoology, Chinese Academy of Sciences
Guangyi Fan: BGI-Qingdao, BGI-Shenzhen
Jinhuan Wang: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
Fan Zhou: Frasergen Bioinformatics Co., Ltd
Wenhui Nie: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences
Chenzhou Zhang: Northwestern Polytechnical University
Lin Liu: Frasergen Bioinformatics Co., Ltd
Zhenyu Zhong: Beijing Milu Ecological Research Center
Wenbo Zhu: Northwestern Polytechnical University
Guichun Liu: Northwestern Polytechnical University
Zeshan Lin: Northwestern Polytechnical University
Chang Liu: Northwestern Polytechnical University
Jiong Zhou: Northwestern Polytechnical University
Guangping Huang: Institute of Zoology, Chinese Academy of Sciences
Zihe Li: Northwestern Polytechnical University
Jianping Yu: Qianjiangyuan National Park
Yaolei Zhang: BGI-Qingdao, BGI-Shenzhen
Yue Yang: Northwestern Polytechnical University
Bingzhao Zhuo: Northwestern Polytechnical University
Baowei Zhang: Anhui University
Jiang Chang: Chinese Research Academy of Environmental Sciences
Haiyuan Qian: Qianjiangyuan National Park
Yingmei Peng: Northwestern Polytechnical University
Xianqing Chen: Northwestern Polytechnical University
Lei Chen: Northwestern Polytechnical University
Zhipeng Li: Jilin Agricultural University
Qi Zhou: MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University
Wen Wang: Northwestern Polytechnical University
Fuwen Wei: Institute of Zoology, Chinese Academy of Sciences

Nature Communications, 2021, vol. 12, issue 1, 1-15

Abstract: Abstract Muntjac deer have experienced drastic karyotype changes during their speciation, making it an ideal model for studying mechanisms and functional consequences of mammalian chromosome evolution. Here we generated chromosome-level genomes for Hydropotes inermis (2n = 70), Muntiacus reevesi (2n = 46), female and male M. crinifrons (2n = 8/9) and a contig-level genome for M. gongshanensis (2n = 8/9). These high-quality genomes combined with Hi-C data allowed us to reveal the evolution of 3D chromatin architectures during mammalian chromosome evolution. We find that the chromosome fusion events of muntjac species did not alter the A/B compartment structure and topologically associated domains near the fusion sites, but new chromatin interactions were gradually established across the fusion sites. The recently borne neo-Y chromosome of M. crinifrons, which underwent male-specific inversions, has dramatically restructured chromatin compartments, recapitulating the early evolution of canonical mammalian Y chromosomes. We also reveal that a complex structure containing unique centromeric satellite, truncated telomeric and palindrome repeats might have mediated muntjacs’ recurrent chromosome fusions. These results provide insights into the recurrent chromosome tandem fusion in muntjacs, early evolution of mammalian sex chromosomes, and reveal how chromosome rearrangements can reshape the 3D chromatin regulatory conformations during species evolution.

Date: 2021
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DOI: 10.1038/s41467-021-27091-0

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