Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations

Xuming Zhou, Fengming Sun, Shixia Xu, Guangyi Fan, Kangli Zhu, Xin Liu, Yuan Chen, Chengcheng Shi, Yunxia Yang, Zhiyong Huang, Jing Chen, Haolong Hou, Xuejiang Guo, Wenbin Chen, Yuefeng Chen, Xiaohong Wang, Tian Lv, Dan Yang, Jiajian Zhou, Bangqing Huang, Zhengfei Wang, Wei Zhao, Ran Tian, Zhiqiang Xiong, Junxiao Xu, Xinming Liang, Bingyao Chen, Weiqing Liu, Junyi Wang, Shengkai Pan, Xiaodong Fang, Ming Li, Fuwen Wei, Xun Xu, Kaiya Zhou, Jun Wang () and Guang Yang ()
Additional contact information
Xuming Zhou: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University
Fengming Sun: BGI-Shenzhen
Shixia Xu: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University
Guangyi Fan: BGI-Shenzhen
Kangli Zhu: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University
Xin Liu: BGI-Shenzhen
Yuan Chen: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University
Chengcheng Shi: BGI-Shenzhen
Yunxia Yang: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University
Zhiyong Huang: BGI-Shenzhen
Jing Chen: BGI-Shenzhen
Haolong Hou: BGI-Shenzhen
Xuejiang Guo: State Key Laboratory of Reproductive Medicine, Nanjing Medical University
Wenbin Chen: BGI-Shenzhen
Yuefeng Chen: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University
Xiaohong Wang: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University
Tian Lv: BGI-Shenzhen
Dan Yang: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University
Jiajian Zhou: BGI-Shenzhen
Bangqing Huang: BGI-Shenzhen
Zhengfei Wang: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University
Wei Zhao: BGI-Shenzhen
Ran Tian: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University
Zhiqiang Xiong: BGI-Shenzhen
Junxiao Xu: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University
Xinming Liang: BGI-Shenzhen
Bingyao Chen: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University
Weiqing Liu: BGI-Shenzhen
Junyi Wang: BGI-Shenzhen
Shengkai Pan: BGI-Shenzhen
Xiaodong Fang: BGI-Shenzhen
Ming Li: Institute of Zoology, Chinese Academy of Sciences
Fuwen Wei: Institute of Zoology, Chinese Academy of Sciences
Xun Xu: BGI-Shenzhen
Kaiya Zhou: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University
Jun Wang: BGI-Shenzhen
Guang Yang: Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University

Nature Communications, 2013, vol. 4, issue 1, 1-6

Abstract: Abstract The baiji, or Yangtze River dolphin (Lipotes vexillifer), is a flagship species for the conservation of aquatic animals and ecosystems in the Yangtze River of China; however, this species has now been recognized as functionally extinct. Here we report a high-quality draft genome and three re-sequenced genomes of L. vexillifer using Illumina short-read sequencing technology. Comparative genomic analyses reveal that cetaceans have a slow molecular clock and molecular adaptations to their aquatic lifestyle. We also find a significantly lower number of heterozygous single nucleotide polymorphisms in the baiji compared to all other mammalian genomes reported thus far. A reconstruction of the demographic history of the baiji indicates that a bottleneck occurred near the end of the last deglaciation, a time coinciding with a rapid decrease in temperature and the rise of eustatic sea level.

Date: 2013
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DOI: 10.1038/ncomms3708

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