{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,4]],"date-time":"2026-10-04T03:53:48Z","timestamp":1791086028517,"version":"4.1.0"},"reference-count":60,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2025,5,6]],"date-time":"2025-05-06T00:00:00Z","timestamp":1746489600000},"content-version":"vor","delay-in-days":6,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"JSPS KAKENHI","award":["22H04925"],"award-info":[{"award-number":["22H04925"]}]},{"name":"JSPS KAKENHI","award":["22H02598"],"award-info":[{"award-number":["22H02598"]}]},{"name":"JSPS KAKENHI","award":["23K18093"],"award-info":[{"award-number":["23K18093"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,4,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The XX\/XY sex chromosome system is highly conserved across mammals, with rare exceptions where males lack a Y chromosome. Among these is the genus Tokudaia, a group of spiny rats comprising three species with unique sex chromosome systems deviating from the typical XX\/XY pattern. While Tokudaia osimensis and Tokudaia tokunoshimensis have completely lost the Y chromosome, they retain some Y-linked genes on the X chromosome. In contrast, Tokudaia muenninki retains large sex chromosomes where both the X and Y chromosomes have fused with an autosome pair, carrying multi-copied Y-linked genes, including Sry. In this study, we generated chromosome-level genome assemblies for male individuals of all three Tokudaia species. By investigating loci typically associated with rodent Y-linked genes, we characterized sequences derived from the Tokudaia Y-chromosomal most recent common ancestor (Tokudaia Y-MRCA) and traced their evolutionary trajectories. Our analyses revealed that an initial X-to-Y translocation of a sequence containing the boundary-associated segmental duplication in a common ancestor of Tokudaia marked the beginning of their unique sex chromosome evolution. The boundary-associated segmental duplication, uniquely multi-copied in Tokudaia, facilitated further rearrangements through nonallelic homologous recombination and duplications. These processes culminated in subsequent Y-to-X translocations and duplications, leading to the complete loss of the Y chromosome as a distinct entity while preserving Y-linked genes in a multicopy state on the X chromosome. These findings highlight Tokudaia's rapid sex chromosome evolution within 3 million years and provide insights into the mechanisms underlying Y chromosome loss, contributing to a broader understanding of sex chromosome evolution in rodents.<\/jats:p>","DOI":"10.1093\/molbev\/msaf102","type":"journal-article","created":{"date-parts":[[2025,5,6]],"date-time":"2025-05-06T17:04:02Z","timestamp":1746551042000},"source":"Crossref","is-referenced-by-count":4,"title":["Where Did the Y Chromosome in the Spiny Rat Go, and How Did It Get There?"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6164-1878","authenticated-orcid":false,"given":"Miki","family":"Okuno","sequence":"first","affiliation":[{"name":"Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine , Kurume, Fukuoka 830-0011 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6503-3880","authenticated-orcid":false,"given":"Kentaro","family":"Matsuoka","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, Institute of Science Tokyo , Tokyo 152-8550 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6096-064X","authenticated-orcid":false,"given":"Yuta","family":"Mochimaru","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, Institute of Science Tokyo , Tokyo 152-8550 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0541-2325","authenticated-orcid":false,"given":"Takahiro","family":"Yamabe","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, Institute of Science Tokyo , Tokyo 152-8550 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-5283-8464","authenticated-orcid":false,"given":"Mayou","family":"Okano","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, Institute of Science Tokyo , Tokyo 152-8550 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7388-6856","authenticated-orcid":false,"given":"Takamichi","family":"Jogahara","sequence":"additional","affiliation":[{"name":"Faculty of Law, Economics and Management, Okinawa University , Naha, Okinawa 902-8521 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0728-7548","authenticated-orcid":false,"given":"Atsushi","family":"Toyoda","sequence":"additional","affiliation":[{"name":"Comparative Genomics Laboratory, National Institute of Genetics , Mishima, Shizuoka 411-8540 ,","place":["Japan"]},{"name":"Advanced Genomics Center, National Institute of Genetics , Mishima, Shizuoka 411-8540 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3942-3372","authenticated-orcid":false,"given":"Asato","family":"Kuroiwa","sequence":"additional","affiliation":[{"name":"Reproductive and Developmental Science, Biosystems Science Course, Graduate School of Life Science, Hokkaido University , Sapporo, Hokkaido 060-0810 ,","place":["Japan"]},{"name":"Division of Reproductive and Developmental Biology, Department of Biological Sciences, Faculty of Science, Hokkaido University , Sapporo, Hokkaido 060-0810 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6113-557X","authenticated-orcid":false,"given":"Takehiko","family":"Itoh","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, Institute of Science Tokyo , 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