气候变化领域集成服务门户(CCPortal): Chromosome-scale genomes provide new insights into subspecies divergence and evolutionary characteristics of the giant panda

CCPortal

DOI	10.1016/j.scib.2021.02.002
	Chromosome-scale genomes provide new insights into subspecies divergence and evolutionary characteristics of the giant panda
	Guang X.; Lan T.; Wan Q.-H.; Huang Y.; Li H.; Zhang M.; Li R.; Zhang Z.; Lei Y.; Zhang L.; Zhang H.; Li D.; Li X.; Li H.; Xu Y.; Qiao M.; Wu D.; Tang K.; Zhao P.; Lin J.-Q.; Kumar Sahu S.; Liang Q.; Jiang W.; Zhang D.; Xu X.; Liu X.; Lisby M.; Yang H.; Kristiansen K.; Liu H.; Fang S.-G.
发表日期	2021
ISSN	20959273
英文摘要	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. © 2021 Science China Press
关键词	Chromosome-level genome Divergence time Giant panda Inner organ size Reduced fertility
英文关键词	Transcription; Body sizes; Chromosome-level genome; Divergence time; Giant panda; High quality; Inner organ size; Reduced fertility; Regulatory elements; Sichuan; Species specifics; Cell proliferation
语种	英语
来源期刊	Science Bulletin
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/207404
作者单位	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, 100029, China; Qinling Research Center of Giant Panda Breeding, Shaanxi Academy of Forestry, Xian, 710082, China; China Wildlife Conservation Association, Beijing, 100714, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, DK-2100, Denmark; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China; Guangdong Provincial Academici...
推荐引用方式 GB/T 7714	Guang X.,Lan T.,Wan Q.-H.,et al. Chromosome-scale genomes provide new insights into subspecies divergence and evolutionary characteristics of the giant panda[J],2021.
APA	Guang X..,Lan T..,Wan Q.-H..,Huang Y..,Li H..,...&Fang S.-G..(2021).Chromosome-scale genomes provide new insights into subspecies divergence and evolutionary characteristics of the giant panda.Science Bulletin.
MLA	Guang X.,et al."Chromosome-scale genomes provide new insights into subspecies divergence and evolutionary characteristics of the giant panda".Science Bulletin (2021).