{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T16:49:34Z","timestamp":1789145374666,"version":"build-2803163510"},"reference-count":0,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2024,12,12]],"date-time":"2024-12-12T00:00:00Z","timestamp":1733961600000},"content-version":"vor","delay-in-days":11,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2022YFF1000100"],"award-info":[{"award-number":["2022YFF1000100"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project","award":["2022GD-TSLD-46-0401"],"award-info":[{"award-number":["2022GD-TSLD-46-0401"]}]},{"name":"Key Science and Technology Projects of Xinjiang Uygur Autonomous Region","award":["2024A02004"],"award-info":[{"award-number":["2024A02004"]}]},{"DOI":"10.13039\/501100001809","name":"National Science Foundation of China","doi-asserted-by":"publisher","award":["U23A20228"],"award-info":[{"award-number":["U23A20228"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Design and Breeding of New High-Quality Disease-Resistant Cashmere Goat Varieties","award":["2023ZD04051"],"award-info":[{"award-number":["2023ZD04051"]}]},{"name":"Science and Technology Innovation Team","award":["20221100619"],"award-info":[{"award-number":["20221100619"]}]},{"name":"Key Research Program of Core Technology of Shannxi Province","award":["2024NC2-GJHX-09"],"award-info":[{"award-number":["2024NC2-GJHX-09"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>","DOI":"10.1093\/molbev\/msae251","type":"journal-article","created":{"date-parts":[[2024,12,12]],"date-time":"2024-12-12T15:21:38Z","timestamp":1734016898000},"source":"Crossref","is-referenced-by-count":23,"title":["A Graph-based Goat Pangenome Reveals Structural Variations Involved in Domestication and Adaptation"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3948-4052","authenticated-orcid":false,"given":"Peipei","family":"Bian","sequence":"first","affiliation":[{"name":"Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University , Yangling, Shaanxi 712100 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