ArticleMolecular biology and evolution2024
A Graph-based Goat Pangenome Reveals Structural Variations Involved in Domestication and Adaptation.
Article in Molecular biology and evolution, 2024. 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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17 citing papers in PubMed.
- Genetic origin and forensic analysis of han populations from four districts in Shanghai, China, based on Y-chromosome STR and SNP markers.International journal of legal medicine · 2026Article
- Pan-genomics and multi-omics for deciphering genetic variation and accelerating genetic improvement in ruminant livestock.Functional & integrative genomics · 2026Review
- Large-scale human genomic resources drive innovations toward forensic intelligent source attribution and precision identification.International journal of legal medicine · 2026Review
- Interchromosomal Translocations and Large Deletions Drive the Evolution of the Outlier Chromosome in the Smallest Photosynthetic Eukaryote.Genome biology and evolution · 2026Article
- The Pan-Genome of 1107 Spotted Sea Bass Accessions Reveals Gene Evolution Patterns During Domestication Selection.Molecular ecology resources · 2026Article
- Genomic and Phenotypic Differentiation of Ardi Goat Lines with Distinct Facial Pigmentation in Bahrain: Implications for Conservation.Animals : an open access journal from MDPI · 2026Article
- Pangenomics for Agricultural Breeding: Construction Strategies, Evidence Integration, and Translational Constraints.Biology · 2026Review
- Contrasting ancestry patterns inferred from Y chromosome and mitochondrial DNA in Nanjing people from southwestern China.Human genetics · 2026Article
- Tracing the genetic legacy of Altaic-speaking populations suggested long-distance migration and multi-source admixture shape the genomic diversity of Xibe and Daur.Human genetics · 2026Article
- Pan-3D Genome Analysis Reveals the Roles of Structural Variation in Chicken Chromatin Architectures, Domestication and Production Traits.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Population-level structural variant characterization using pangenome graphs.Nature genetics · 2026Article
- Editorial: Genomic insights into sheep and goat breeding efficiency, volume II.Frontiers in veterinary science · 2026Article
- Differentiating the demographic histories and local adaptations of middle-altitude Qiang and Tibetan people.Human genetics · 2025Article
- Whole-genome sequencing reveals complex structural variations at a major locus linked to pigmented spot sizes in Tianfu goats.BMC genomics · 2025Article
- Review
- A comprehensive water buffalo pangenome reveals extensive structural variation linked to population-specific signatures of selection.GigaScience · 2025Article
- Omics in mini-livestock: a genomic perspective on the future of sustainable food systems.Frontiers in genetics · 2025Review
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22 authors.
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Abstract
Pangenomes can facilitate a deeper understanding of genome complexity. Using de novo phased long-read assemblies of eight representative goat breeds, we constructed a graph-based pangenome of goats (Capra hircus) and discovered 113-Mb autosomal novel sequences. Combining this multi-assembly pangenome with low-coverage PacBio HiFi sequences, we constructed a long-read structural variations (SVs) database containing 59,325 SV deletions, 84,910 SV insertions, and 24,954 other complex SV alleles. This resource allowed reliable graph-based genotyping from short reads of 79 wild and 1,148 worldwide domestic goats. Selection signal analysis of SV captured a novel immune-related domestication locus containing the galectin-9 gene and extra copies of the ruminant-specific galectin-9-like genes (LGALS9L), which have high tissue specificity. A segmental duplication in domestic goats generates three additional LGALS9L copies. Ancient goat genome sequences show a gradual increase in frequency of this duplication from the Neolithic to the present. Two other newly detected SVs also have higher selection signals than adjacent SNPs, a truncated-LINE1 deletion in EDAR2 associated with cashmere production and a VNTR-related insertion in PAPSS2 linked to high-altitude adaptation. In summary, the multi-assembly goat pangenome and long-read SV database facilitates detecting complex variations that are important in evolution and selection.
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