摘要
Extant giant pandas are divided into Sichuan and Qinling subspecies.The giant panda has many speciesspecific characteristics,including comparatively small organs for body size,small genitalia of male individuals,and low reproduction.Here,we report the most contiguous,high-quality chromosomelevel 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.
现生的大熊猫包含两个亚种——四川亚种和秦岭亚种.本研究利用第三代基因组测序技术在染色体层次上组装了迄今为止最为完整的大熊猫两个亚种的基因组,且秦岭亚种的基因组为首次组装.通过对25只大熊猫的高深度测序和分化时间的估算,发现大熊猫四川亚种和秦岭亚种之间的分化时间在距今约1.0到1.2万年前.进一步的比较基因组分析发现,大熊猫基因组上DACH2基因调控元件的特异性丢失以及SYT6基因的特异性位点突变是大熊猫较其他哺乳动物的繁殖率低的重要原因之一,而四川亚种IQCD基因正选择进化的结果则是四川亚种比秦岭亚种具有较高繁殖率的主要原因之一.最后,本研究发现大熊猫Hippo通路上诸基因的快速进化和一些基因调控元件上的特异性突变位点,可能是导致大熊猫具有较小的内脏器官以应对食性改变和减少能量代谢的适应性进化结果.
作者
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
Xiaoping Li
Haimeng Li
Yan Xu
Maiju Qiao
Daifu Wu
Keyi Tang
Pengpeng Zhao
Jian-Qing Lin
Sunil KumarSahu
Qiqi Liang
Wenkai Jiang
Danhui Zhang
Xun Xu
Xin Liu
Michael Lisby
Huanming Yang
Karsten Kristiansen
Huan Liu
Sheng-Guo Fang
光宣敏;兰天明;万秋红;黄炎;李洪;张明春;李仁贵;张志忠;雷颖虎;张玲;张和民;李德生;李晓平;李海盟;徐妍;乔麦菊;吴代福;唐刻意;赵鹏鹏;林剑青;Sunil KumarSahu;梁齐齐;江文凯;张丹辉;徐讯;刘心;Michael Lisby;杨焕明;Karsten Kristiansen;刘欢;方盛国(MOE Key Laboratory of Biosystems Homeostasis&Protection,State Conservation Centre for Gene Resources of Endangered Wildlife,College of Life Sciences,Zhejiang University,Hangzhou 310058,China;State Key Laboratory of Agricultural Genomics,BGI-Shenzhen,Shenzhen 518083,China;Key Laboratory of State Forestry and Grassland Administration(State Park Administration)on Conservation Biology of Rare Animals in the Giant Panda National Park,China,Conservation and Research Center for the Giant Panda,Dujiangyan 611830,China;Novogene Bioinformatics Institute,Beijing 100083,China;Qinling Research Center of Giant Panda Breeding,Shaanxi Academy of Forestry,Xi’an 710082,China;China Wildlife Conservation Association,Beijing 100714,China;Laboratory of Genomics and Molecular Biomedicine,Department of Biology,University of Copenhagen,DK-2100 Copenhagen,Denmark;Guangdong Provincial Key Laboratory of Genome Read and Write,BGI-Shenzhen,Shenzhen 518120,China;Guangdong Provincial Academician Workstation of BGI Synthetic Genomics,BGI-Shenzhen,Shenzhen 518120,China;Qingdao-Europe Advanced Institute for Life Sciences,Qingdao 266555,China)
基金
supported by the National Key Program(2016YFC0503200)from the Ministry of Science and Technology of China
a special grant for the giant panda from the State Forestry Administration of the People’s Republic of China
the Fundamental Research Funds for the Central Universities of the People’s Republic of China
the Foundation of Key Laboratory of State Forestry and Grassland Administration(State Park Administration)on Conservation Biology of Rare Animals in the Giant Panda National Park(KLSFGAGP2020.002)
the Guangdong Provincial Key Laboratory of Genome Read and Write(2017B030301011)。
