{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T22:41:54Z","timestamp":1776897714749,"version":"3.51.2"},"posted":{"date-parts":[[2023,3,3]]},"group-title":"Genomics","reference-count":54,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,3,18]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  Y-chromosomal Ampliconic Genes (YAGs) are important for male fertility, as they encode proteins functioning in spermatogenesis. The variation in copy number and expression levels of these multicopy gene families has been recently studied in great apes, however, the diversity of splicing variants remains unexplored. Here we deciphered the sequences of polyadenylated transcripts of all nine YAG families (\n                  <jats:italic>BPY2<\/jats:italic>\n                  ,\n                  <jats:italic>CDY<\/jats:italic>\n                  ,\n                  <jats:italic>DAZ<\/jats:italic>\n                  ,\n                  <jats:italic>HSFY<\/jats:italic>\n                  ,\n                  <jats:italic>PRY<\/jats:italic>\n                  ,\n                  <jats:italic>RBMY<\/jats:italic>\n                  ,\n                  <jats:italic>TSPY<\/jats:italic>\n                  ,\n                  <jats:italic>VCY<\/jats:italic>\n                  , and\n                  <jats:italic>XKRY<\/jats:italic>\n                  ) from testis samples of six great ape species (human, chimpanzee, bonobo, gorilla, Bornean orangutan, and Sumatran orangutan). To achieve this, we enriched YAG transcripts with capture-probe hybridization and sequenced them with long (Pacific Biosciences) reads. Our analysis of this dataset resulted in several findings. First, we uncovered a high diversity of YAG transcripts across great apes. Second, we observed evolutionarily conserved alternative splicing patterns for most YAG families except for\n                  <jats:italic>BPY2<\/jats:italic>\n                  and\n                  <jats:italic>PRY<\/jats:italic>\n                  . Our results suggest that\n                  <jats:italic>BPY2<\/jats:italic>\n                  transcripts and predicted proteins in several great ape species (bonobo and the two orangutans) have independent evolutionary origins and are not homologous to human reference transcripts and proteins. In contrast, our results suggest that the\n                  <jats:italic>PRY<\/jats:italic>\n                  gene family, having the highest representation of transcripts without open reading frames, has been undergoing pseudogenization. Third, even though we have identified many species-specific protein-coding YAG transcripts, we have not detected any signatures of positive selection. Overall, our work illuminates the YAG isoform landscape and its evolutionary history, and provides a genomic resource for future functional studies focusing on infertility phenotypes in humans and critically endangered great apes.\n                <\/jats:p>","DOI":"10.1101\/2023.03.02.530874","type":"posted-content","created":{"date-parts":[[2023,3,7]],"date-time":"2023-03-07T02:15:23Z","timestamp":1678155323000},"source":"Crossref","is-referenced-by-count":0,"title":["Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes"],"prefix":"10.64898","author":[{"given":"Marta","family":"Tomaszkiewicz","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7378-2320","authenticated-orcid":false,"given":"Kristoffer","family":"Sahlin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul","family":"Medvedev","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kateryna D.","family":"Makova","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2023032113100817000_2023.03.02.530874v2.1","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1007\/978-1-4939-7834-2_6","article-title":"Transcript Profiling Using Long-Read Sequencing Technologies","volume":"1783","year":"2018","journal-title":"Methods in Molecular Biology"},{"key":"2023032113100817000_2023.03.02.530874v2.2","doi-asserted-by":"publisher","DOI":"10.1038\/nature13206"},{"key":"2023032113100817000_2023.03.02.530874v2.3","doi-asserted-by":"publisher","DOI":"10.1101\/gr.5734907"},{"key":"2023032113100817000_2023.03.02.530874v2.4","doi-asserted-by":"crossref","unstructured":"Camacho, Christiam , George Coulouris , Vahram Avagyan , Ning Ma , Jason Papadopoulos , Kevin Bealer , and Thomas L. 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Zaidi , Marta Tomaszkiewicz , Kate Anthony , Corey Liebowitz , Michael DeGiorgio , Mark D. Shriver , and Kateryna D. Makova . 2018. \u201cHigh Levels of Copy Number Variation of Ampliconic Genes across Major Human Y Haplogroups.\u201d Genome Biology and Evolution. https:\/\/doi.org\/10.1093\/gbe\/evy086.","DOI":"10.1101\/230342"},{"key":"2023032113100817000_2023.03.02.530874v2.52","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2605.2004.00469.x"},{"key":"2023032113100817000_2023.03.02.530874v2.53","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msx212"},{"key":"2023032113100817000_2023.03.02.530874v2.54","doi-asserted-by":"crossref","unstructured":"Zou, Sheng Wei , Jian Chao Zhang , Xiao Dong Zhang , Shi Ying Miao , Shu Dong Zong , Qi Sheng , and Lin Fang Wang . 2003. \u201cExpression and Localization of VCX\/Y Proteins and Their Possible Involvement in Regulation of Ribosome Assembly during Spermatogenesis.\u201d Cell Research. https:\/\/doi.org\/10.1038\/sj.cr.7290161.","DOI":"10.1038\/sj.cr.7290161"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2023.03.02.530874","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T04:20:46Z","timestamp":1768450846000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2023.03.02.530874"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,3,3]]},"references-count":54,"URL":"https:\/\/doi.org\/10.1101\/2023.03.02.530874","relation":{"is-preprint-of":[{"id-type":"doi","id":"10.1093\/gbe\/evad205","asserted-by":"subject"}]},"subject":[],"published":{"date-parts":[[2023,3,3]]},"subtype":"preprint"}}