{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T04:42:33Z","timestamp":1771476153114,"version":"3.50.1"},"reference-count":82,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2021,1,16]],"date-time":"2021-01-16T00:00:00Z","timestamp":1610755200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Alpaca Research Foundation","award":["2015-2018, 2017-2019"],"award-info":[{"award-number":["2015-2018, 2017-2019"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>The unique evolutionary dynamics and complex structure make the Y chromosome the most diverse and least understood region in the mammalian genome, despite its undisputable role in sex determination, development, and male fertility. Here we present the first contig-level annotated draft assembly for the alpaca (Vicugna pacos) Y chromosome based on hybrid assembly of short- and long-read sequence data of flow-sorted Y. The latter was also used for cDNA selection providing Y-enriched testis transcriptome for annotation. The final assembly of 8.22 Mb comprised 4.5 Mb of male specific Y (MSY) and 3.7 Mb of the pseudoautosomal region. In MSY, we annotated 15 X-degenerate genes and two novel transcripts, but no transposed sequences. Two MSY genes, HSFY and RBMY, are multicopy. The pseudoautosomal boundary is located between SHROOM2 and HSFY. Comparative analysis shows that the small and cytogenetically distinct alpaca Y shares most of MSY sequences with the larger dromedary and Bactrian camel Y chromosomes. Most of alpaca X-degenerate genes are also shared with other mammalian MSYs, though WWC3Y is Y-specific only in alpaca\/camels and the horse. The partial alpaca Y assembly is a starting point for further expansion and will have applications in the study of camelid populations and male biology.<\/jats:p>","DOI":"10.3390\/genes12010105","type":"journal-article","created":{"date-parts":[[2021,1,18]],"date-time":"2021-01-18T05:17:34Z","timestamp":1610947054000},"page":"105","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3874-4991","authenticated-orcid":false,"given":"Matthew J.","family":"Jevit","sequence":"first","affiliation":[{"name":"Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&amp;M University, College Station, TX 77843-4458, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6121-135X","authenticated-orcid":false,"given":"Brian W.","family":"Davis","sequence":"additional","affiliation":[{"name":"Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&amp;M University, College Station, TX 77843-4458, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5910-9666","authenticated-orcid":false,"given":"Caitlin","family":"Castaneda","sequence":"additional","affiliation":[{"name":"Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&amp;M University, College Station, TX 77843-4458, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4874-7077","authenticated-orcid":false,"given":"Andrew","family":"Hillhouse","sequence":"additional","affiliation":[{"name":"Molecular Genomics Workplace, Institute for Genome Sciences and Society, Texas A&amp;M University, College Station, TX 77843-4458, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7385-0618","authenticated-orcid":false,"given":"Rytis","family":"Juras","sequence":"additional","affiliation":[{"name":"Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&amp;M University, College Station, TX 77843-4458, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0454-8359","authenticated-orcid":false,"given":"Vladimir A.","family":"Trifonov","sequence":"additional","affiliation":[{"name":"Laboratory of Comparative Genomics, Institute of Molecular and Cellular Biology, 630090 Novosibirsk, Russia"}]},{"given":"Ahmed","family":"Tibary","sequence":"additional","affiliation":[{"name":"Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164-6610, USA"}]},{"given":"Jorge C.","family":"Pereira","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9372-1381","authenticated-orcid":false,"given":"Malcolm A.","family":"Ferguson-Smith","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2276-475X","authenticated-orcid":false,"given":"Terje","family":"Raudsepp","sequence":"additional","affiliation":[{"name":"Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&amp;M University, College Station, TX 77843-4458, USA"}]}],"member":"1968","published-online":{"date-parts":[[2021,1,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"964","DOI":"10.1126\/science.286.5441.964","article-title":"Four evolutionary strata on the human X chromosome","volume":"286","author":"Lahn","year":"1999","journal-title":"Science"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1146\/annurev.genet.42.110807.091714","article-title":"Weird Animal Genomes and the Evolution of Vertebrate Sex and Sex Chromosomes","volume":"42","author":"Graves","year":"2008","journal-title":"Annu. 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