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Chromosome-scale genomes reveal genomic consequences of inbreeding in the South China tiger: A comparative study with the Amur tiger |
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| Authors: | Le Zhang Tianming Lan Chuyu Lin Wenyuan Fu Yaohua Yuan Kaixiong Lin Haimeng Li Sunil Kumar Sahu Zhaoyang Liu Daqing Chen Qunxiu Liu Aishan Wang Xiaohong Wang Yue Ma Shizhou Li Yixin Zhu Xingzhuo Wang Xiaotong Ren Haorong Lu Yunting Huang Jieyao Yu Boyang Liu Qing Wang Shaofang Zhang Xun Xu Huanming Yang Dan Liu Huan Liu Yanchun Xu |
| Affiliation: | 1. College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China;2. State Key Laboratory of Agricultural Genomics, Shenzhen, China;3. Shenzhen Zhong Nong Jing Yue Biotech Company Limited, Shenzhen, China;4. Longyan Geopark Protection and Development Center, Longyan, China Fujian Meihuashan Institute of South China Tiger Breeding, Longyan, China;5. Shanghai Zoological Park, Shanghai, China;6. Fujian Meihuashan Institute of South China Tiger Breeding, Longyan, China;7. State Key Laboratory of Agricultural Genomics, Shenzhen, China College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China;8. Luoyang Zoo in Wangcheng Park, Luoyang, China;9. Suzhou Shangfangshan Forest Zoo, Suzhou, China;10. Nanchang Zoo, Nanchang, China;11. Shaoguan Research Base of South China Tiger, Shaoguan, China;12. China National GeneBank, Shenzhen, China Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China;13. China National GeneBank, Shenzhen, China;14. Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China;15. Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, Shenzhen, China James D. Watson Institute of Genome Sciences, Hangzhou, China;16. Heilongjiang Siberian Tiger Park, Harbin, China |
| Abstract: | The South China tiger (Panthera tigris amoyensis, SCT) is the most critically endangered subspecies of tiger due to functional extinction in the wild. Inbreeding depression is observed among the captive population descended from six wild ancestors, resulting in high juvenile mortality and low reproduction. We assembled and characterized the first SCT genome and an improved Amur tiger (P. t. altaica, AT) genome named AmyTig1.0 and PanTig2.0. The two genomes are the most continuous and comprehensive among any tiger genomes yet reported at the chromosomal level. By using the two genomes and resequencing data of 15 SCT and 13 AT individuals, we investigated the genomic signature of inbreeding depression of the SCT. The results indicated that the effective population size of SCT experienced three phases of decline, ~5.0–1.0 thousand years ago, 100 years ago, and since captive breeding in 1963. We found 43 long runs of homozygosity fragments that were shared by all individuals in the SCT population and covered a total length of 20.63% in the SCT genome. We also detected a large proportion of identical-by-descent segments across the genome in the SCT population, especially on ChrB4. Deleterious nonsynonymous single nucleotide polymorphic sites and loss-of-function mutations were found across genomes with extensive potential influences, despite a proportion of these loads having been purged by inbreeding depression. Our research provides an invaluable resource for the formulation of genetic management policies for the South China tiger such as developing genome-based breeding and genetic rescue strategy. |
| Keywords: | Amur tiger genetic management inbreeding depression South China tiger |