The First High-Quality Reference Genome of Sika Deer Provides Insights into High-Tannin Adaptation

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  • Xiumei Xing
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Cheng Ai
    Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, 518120 , China
  • Tianjiao Wang
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Yang Li
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Huitao Liu
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Pengfei Hu
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Guiwu Wang
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Huamiao Liu
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Hongliang Wang
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Ranran Zhang
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Junjun Zheng
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Xiaobo Wang
    Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, 518120 , China
  • Lei Wang
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Yuxiao Chang
    Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, 518120 , China
  • Qian Qian
    Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, 518120 , China
  • Jinghua Yu
    CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences , Shenyang, 110016 , China
  • Lixin Tang
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Shigang Wu
    Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, 518120 , China
  • Xiujuan Shao
    Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, 518120 , China
  • Alun Li
    Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, 518120 , China
  • Peng Cui
    Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, 518120 , China
  • Wei Zhan
    Annoroad Gene Technology (Beijing) Co., Ltd , Beijing, 100176 , China
  • Sheng Zhao
    Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, 518120 , China
  • Zhichao Wu
    Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, 518120 , China
  • Xiqun Shao
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Yimeng Dong
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Min Rong
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Yihong Tan
    CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences , Shenyang, 110016 , China
  • Xuezhe Cui
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Shuzhuo Chang
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Xingchao Song
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Tongao Yang
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Limin Sun
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Yan Ju
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Pei Zhao
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Huanhuan Fan
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Ying Liu
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Xinhui Wang
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Wanyun Yang
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Min Yang
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Tao Wei
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Shanshan Song
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Jiaping Xu
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Zhigang Yue
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Qiqi Liang
    Novogene Bioinformatics Institute , Beijing, 100083 , China
  • Chunyi Li
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China
  • Jue Ruan
    Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences , Shenzhen, 518120 , China
  • Fuhe Yang
    Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals, Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences , Changchun, 130112 , China

抄録

<jats:title>Abstract</jats:title> <jats:p>Sika deer are known to prefer oak leaves, which are rich in tannins and toxic to most mammals; however, the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear. In identifying the mechanism responsible for the tolerance of a highly toxic diet, we have made a major advancement by explaining the genome of sika deer. We generated the first high-quality, chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments. Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food, especially the expansion of the UGT family 2 subfamily B of UGT genes. The first chromosome-level assembly and genetic characterization of the tolerance to a highly toxic diet suggest that the sika deer genome may serve as an essential resource for understanding evolutionary events and tannin adaptation. Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.</jats:p>

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