Chromosome-scale genomes provide new insights into subspecies divergence and evolutionary characteristics of the giant panda

Research output: Contribution to journalJournal articleResearchpeer-review

  • Xuanmin Guang
  • Tianming Lan
  • Qiu Hong Wan
  • Yan Huang
  • Hong Li
  • Mingchun Zhang
  • Rengui Li
  • Zhizhong Zhang
  • Yinghu Lei
  • Ling Zhang
  • Heming Zhang
  • Desheng Li
  • Haimeng Li
  • Yan Xu
  • Maiju Qiao
  • Daifu Wu
  • Keyi Tang
  • Pengpeng Zhao
  • Jian-Qing Lin
  • Sunil Kumar Sahu
  • Qiqi Liang
  • Wenkai Jiang
  • Danhui Zhang
  • Xun Xu
  • Xin Liu
  • Huanming Yang
  • Sheng-Guo Fang

Extant giant pandas are divided into Sichuan and Qinling subspecies. The giant panda has many species-specific characteristics, including comparatively small organs for body size, small genitalia of male individuals, and low reproduction. Here, we report the most contiguous, high-quality chromosome-level genomes of two extant giant panda subspecies to date, with the first genome assembly of the Qinling subspecies. Compared with the previously assembled giant panda genomes based on short reads, our two assembled genomes increased contiguity over 200-fold at the contig level. Additional sequencing of 25 individuals dated the divergence of the Sichuan and Qinling subspecies into two distinct clusters from 10,000 to 12,000 years ago. Comparative genomic analyses identified the loss of regulatory elements in the dachshund family transcription factor 2 (DACH2) gene and specific changes in the synaptotagmin 6 (SYT6) gene, which may be responsible for the reduced fertility of the giant panda. Positive selection analysis between the two subspecies indicated that the reproduction-associated IQ motif containing D (IQCD) gene may at least partly explain the different reproduction rates of the two subspecies. Furthermore, several genes in the Hippo pathway exhibited signs of rapid evolution with giant panda-specific variants and divergent regulatory elements, which may contribute to the reduced inner organ sizes of the giant panda.

Original languageEnglish
JournalScience Bulletin
Issue number19
Pages (from-to)2002-2013
Number of pages12
Publication statusPublished - 2021

    Research areas

  • Chromosome-level genome, Divergence time, Giant panda, Inner organ size, Reduced fertility

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