Population genomic analysis provides evidence of the past success and future potential of South China tiger captive conservation

文献类型： 外文期刊

第一作者： Wang, Chen

作者： Wang, Chen;Wu, Ya-Jiang;Shan, Fen;Li, Wan-Ping;Zhai, Jun-Qiong;Huang, Mian;Peng, Shi-Ming;Cai, Qin-Hui;Chen, Wu;Wang, Chen;Wu, Ya-Jiang;Shan, Fen;Li, Wan-Ping;Zhai, Jun-Qiong;Huang, Mian;Peng, Shi-Ming;Cai, Qin-Hui;Chen, Wu;Wu, Dong-Dong;Yao, Meng-Cheng;Tu, Xiao-Long;Wu, Dong-Dong;Yao, Meng-Cheng;Tu, Xiao-Long;Wu, Dong-Dong;Yao, Meng-Cheng;Tu, Xiao-Long;Yuan, Yao-Hua;Yu, Jian-Yi;Liu, Qun-Xiu;Han, Jian-Lin;Han, Jian-Lin;Liu, Zhao-Yang;Li, Lin-Xiang;Teng, Ming-Sheng

作者机构：

关键词： South China tiger; Chromosome-level genome; Whole genome sequencing; Genomic inbreeding; Deleterious mutations

期刊名称：BMC BIOLOGY （ 影响因子：5.4； 五年影响因子：7.1 ）

ISSN：

年卷期： 2023 年 21 卷 1 期

页码：

收录情况： SCI

摘要： BackgroundAmong six extant tiger subspecies, the South China tiger (Panthera tigris amoyensis) once was widely distributed but is now the rarest one and extinct in the wild. All living South China tigers are descendants of only two male and four female wild-caught tigers and they survive solely in zoos after 60 years of effective conservation efforts. Inbreeding depression and hybridization with other tiger subspecies were believed to have occurred within the small, captive South China tiger population. It is therefore urgently needed to examine the genomic landscape of existing genetic variation among the South China tigers.ResultsIn this study, we assembled a high-quality chromosome-level genome using long-read sequences and re-sequenced 29 high-depth genomes of the South China tigers. By combining and comparing our data with the other 40 genomes of six tiger subspecies, we identified two significantly differentiated genomic lineages among the South China tigers, which harbored some rare genetic variants introgressed from other tiger subspecies and thus maintained a moderate genetic diversity. We noticed that the South China tiger had higher F-ROH values for longer runs of homozygosity (ROH > 1 Mb), an indication of recent inbreeding/founder events. We also observed that the South China tiger had the least frequent homozygous genotypes of both high- and moderate-impact deleterious mutations, and lower mutation loads than both Amur and Sumatran tigers. Altogether, our analyses indicated an effective genetic purging of deleterious mutations in homozygous states from the South China tiger, following its population contraction with a controlled increase in inbreeding based on its pedigree records.ConclusionsThe identification of two unique founder/genomic lineages coupled with active genetic purging of deleterious mutations in homozygous states and the genomic resources generated in our study pave the way for a genomics-informed conservation, following the real-time monitoring and rational exchange of reproductive South China tigers among zoos.

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