ArticleMolecular ecology resources2023
Chromosome-scale genomes reveal genomic consequences of inbreeding in the South China tiger: A comparative study with the Amur tiger.
Article in Molecular ecology resources, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 29 citations in OpenAlex.
- MitoNumt: A Workflow for Recovering Mitochondrial Genomes From Long-Read Data and Detecting NUMT Contamination in Mitochondrial Genome Assemblies.Molecular ecology resources · 2026Article
- Assessment of High Throughput Sequencing Quality of Host DNA Enriched From Faeces: A Case From Captive Tiger.Molecular ecology resources · 2026Article
- Comparative Histopathological and Morphometric Analysis of Lung Tissues in Stillborn Cubs of South China Tiger and Amur Tiger.Biology · 2025Article
- Population Genomics Provides Insights Into Genomic Features of Inbreeding Depression inEvolutionary applications · 2025Review
- Runs of Homozygosity and Inferences in Wild Populations.Molecular ecology · 2025Review
- Enhancing inbreeding estimation and global conservation insights through chromosome-level assemblies of the Chinese and Malayan pangolin.GigaScience · 2025Article
- Revealing Amur tiger family pedigrees based on age identification using fecal microbiome and kinship analysis.Frontiers in microbiology · 2025Article
- Large-scale genome sequencing of giant pandas improves the understanding of population structure and future conservation initiatives.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Genome sequencing of captive white tigers from Bangladesh.BMC genomic data · 2024Article
- A chromosome-scale fishing cat reference genome for the evaluation of potential germline risk variants.Scientific reports · 2024Article
- Insights for the Captive Management of South China Tigers Based on a Large-Scale Genetic Survey.Genes · 2024Article
- Haplotype-resolved chromosome-scale genomes of the Asian and African Savannah Elephants.Scientific data · 2024Article
- Telomere-to-telomere gap-free genome assembly of the endangered Yangtze finless porpoise and East Asian finless porpoise.GigaScience · 2024Article
- Population genomic analysis provides evidence of the past success and future potential of South China tiger captive conservation.BMC biology · 2023Article
- The year of the tiger and the year of tiger genomes!Molecular ecology resources · 2023Article
- Chromosome-scale genomes reveal genomic consequences of inbreeding in the South China tiger: A comparative study with the Amur tiger.Molecular ecology resources · 2023Article
- New Evidence of Tiger Subspecies Differentiation and Environmental Adaptation: Comparison of the Whole Genomes of the Amur Tiger and the South China Tiger.Animals : an open access journal from MDPI · 2022Article
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Authors and funding
29 authors at 12 institutions in 1 country.
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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.
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