{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T19:45:38Z","timestamp":1768506338061,"version":"3.49.0"},"posted":{"date-parts":[[2023,5,3]]},"group-title":"Evolutionary Biology","reference-count":51,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,5,3]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  Most eukaryotic genes have been vertically transmitted to the present from distant ancestors. However, variable gene number across species indicates that gene gain and loss also occurs. While new genes typically originate as products of duplications and rearrangements of pre-existing genes, putative\n                  <jats:italic>de novo<\/jats:italic>\n                  genes - genes born out of previously non-genic sequence - have been identified. Previous studies of\n                  <jats:italic>de novo<\/jats:italic>\n                  genes in\n                  <jats:italic>Drosophila<\/jats:italic>\n                  have provided evidence that expression in male reproductive tissues is common. However, no studies have focused on female reproductive tissues. Here we begin addressing this gap in the literature by analyzing the transcriptomes of three female reproductive tract organs (spermatheca, seminal receptacle, and parovaria) in three species - our focal species,\n                  <jats:italic>D. melanogaster<\/jats:italic>\n                  - and two closely related species,\n                  <jats:italic>D. simulans<\/jats:italic>\n                  and\n                  <jats:italic>D. yakuba<\/jats:italic>\n                  , with the goal of identifying putative\n                  <jats:italic>D. melanogaster<\/jats:italic>\n                  -specific\n                  <jats:italic>de novo<\/jats:italic>\n                  genes expressed in these tissues. We discovered several candidate genes, which, consistent with the literature, tend to be short, simple, and lowly expressed. We also find evidence that some of these genes are expressed in other\n                  <jats:italic>D. melanogaster<\/jats:italic>\n                  tissues and both sexes. The relatively small number of candidate genes discovered here is similar to that observed in the accessory gland, but substantially fewer than that observed in the testis.\n                <\/jats:p>","DOI":"10.1101\/2023.05.03.539262","type":"posted-content","created":{"date-parts":[[2023,5,4]],"date-time":"2023-05-04T02:20:12Z","timestamp":1683166812000},"source":"Crossref","is-referenced-by-count":0,"title":["Identifying candidate\n                  <i>de novo<\/i>\n                  genes expressed in the somatic female reproductive tract of\n                  <i>Drosophila melanogaster<\/i>"],"prefix":"10.64898","author":[{"given":"Kaelina D.","family":"Lombardo","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hayley K.","family":"Sheehy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julie M.","family":"Cridland","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David J.","family":"Begun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2023050608500526000_2023.05.03.539262v1.1","doi-asserted-by":"publisher","DOI":"10.1242\/dev.015156"},{"issue":"3","key":"2023050608500526000_2023.05.03.539262v1.2","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1093\/molbev\/msx311","article-title":"De novo Gene Evolution of Antifreeze Glycoproteins in Codfishes Revealed by Whole Genome Sequence Data","volume":"35","year":"2018","journal-title":"Molecular Biology and Evolution"},{"key":"2023050608500526000_2023.05.03.539262v1.3","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.106.069245"},{"key":"2023050608500526000_2023.05.03.539262v1.4","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.105.050336"},{"key":"2023050608500526000_2023.05.03.539262v1.5","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.107.084491"},{"key":"2023050608500526000_2023.05.03.539262v1.6","doi-asserted-by":"publisher","DOI":"10.1038\/nature11184"},{"key":"2023050608500526000_2023.05.03.539262v1.7","doi-asserted-by":"crossref","unstructured":"Casola, C. (2018). From de novo to \u201cde nono\u201d: The majority of novel protein coding genes identified with phylostratigraphy are old genes or recent duplicates. In Genome Biology and Evolution. https:\/\/doi.org\/10.1093\/gbe\/evy231","DOI":"10.1093\/gbe\/evy231"},{"key":"2023050608500526000_2023.05.03.539262v1.8","doi-asserted-by":"crossref","unstructured":"Cridland, J. M. , Majane, A. C. , Zhao, L. , & Begun, D. J. (2022). Population biology of accessory gland-expressed de novo genes in Drosophila melanogaster. Genetics, 220(1). https:\/\/doi.org\/10.1093\/genetics\/iyab207","DOI":"10.1093\/genetics\/iyab207"},{"key":"2023050608500526000_2023.05.03.539262v1.9","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/30.1.207"},{"key":"2023050608500526000_2023.05.03.539262v1.10","doi-asserted-by":"publisher","DOI":"10.1016\/S0065-2660(08)60173-X"},{"key":"2023050608500526000_2023.05.03.539262v1.11","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1883"},{"key":"2023050608500526000_2023.05.03.539262v1.12","doi-asserted-by":"crossref","unstructured":"Gramates, L. S. , Agapite, J. , Attrill, H. , Calvi, B. R. , Crosby, M. A. , Dos Santos, G. , Goodman, J. L. , Goutte-Gattat, D. , Jenkins, V. K. , Kaufman, T. , Larkin, A. , Matthews, B. B. , Millburn, G. , Strelets, V. B. , & the FlyBase Consortium. (2022). Fly Base: a guided tour of highlighted features. Genetics, 220(4). https:\/\/doi.org\/10.1093\/genetics\/iyac035","DOI":"10.1093\/genetics\/iyac035"},{"issue":"4","key":"2023050608500526000_2023.05.03.539262v1.13","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1007\/s00239-020-09939-z","article-title":"A Continuum of Evolving De novo Genes Drives Protein-Coding Novelty in Drosophila","volume":"88","year":"2020","journal-title":"In Journal of Molecular Evolution"},{"issue":"18","key":"2023050608500526000_2023.05.03.539262v1.14","doi-asserted-by":"crossref","first-page":"1527","DOI":"10.1016\/j.cub.2009.07.049","article-title":"Emergence of a new gene from an intergenic region","volume":"19","year":"2009","journal-title":"Current Biology: CB"},{"issue":"12","key":"2023050608500526000_2023.05.03.539262v1.15","doi-asserted-by":"crossref","first-page":"5752","DOI":"10.1093\/molbev\/msab288","article-title":"New Genes Interacted With Recent Whole-Genome Duplicates in the Fast Stem Growth of Bamboos","volume":"38","year":"2021","journal-title":"Molecular Biology and Evolution"},{"key":"2023050608500526000_2023.05.03.539262v1.16","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkx428"},{"key":"2023050608500526000_2023.05.03.539262v1.17","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg129"},{"key":"2023050608500526000_2023.05.03.539262v1.18","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-019-0201-4"},{"key":"2023050608500526000_2023.05.03.539262v1.19","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab971"},{"key":"2023050608500526000_2023.05.03.539262v1.20","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkx976"},{"key":"2023050608500526000_2023.05.03.539262v1.21","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0509809103"},{"issue":"4","key":"2023050608500526000_2023.05.03.539262v1.22","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1038\/cr.2010.31","article-title":"A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand","volume":"20","year":"2010","journal-title":"In Cell Research"},{"key":"2023050608500526000_2023.05.03.539262v1.23","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"2023050608500526000_2023.05.03.539262v1.24","doi-asserted-by":"publisher","DOI":"10.1038\/nrg1204"},{"key":"2023050608500526000_2023.05.03.539262v1.25","doi-asserted-by":"crossref","unstructured":"Luthra, I. , Chen, X. E. , Jensen, C. , Rafi, A. M. , Salaudeen, A. L. , & de Boer, C. G. (2022). Biochemical activity is the default DNA state in eukaryotes. https:\/\/doi.org\/10.1101\/2022.12.16.520785","DOI":"10.1101\/2022.12.16.520785"},{"key":"2023050608500526000_2023.05.03.539262v1.26","doi-asserted-by":"publisher","DOI":"10.1038\/nature10811"},{"key":"2023050608500526000_2023.05.03.539262v1.27","doi-asserted-by":"publisher","DOI":"10.1126\/science.1187096"},{"issue":"5","key":"2023050608500526000_2023.05.03.539262v1.28","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1016\/j.asd.2013.07.002","article-title":"The morphogenesis of spermathecae and spermathecal glands in Drosophila melanogaster","volume":"42","year":"2013","journal-title":"Arthropod Structure & Development"},{"key":"2023050608500526000_2023.05.03.539262v1.29","doi-asserted-by":"crossref","unstructured":"McDonough-Goldstein, C. E. , Borziak, K. , Pitnick, S. , & Dorus, S. (2021). Drosophila female reproductive tract gene expression reveals coordinated mating responses and rapidly evolving tissue-specific genes. G3, 11(3). https:\/\/doi.org\/10.1093\/g3journal\/jkab020","DOI":"10.1093\/g3journal\/jkab020"},{"key":"2023050608500526000_2023.05.03.539262v1.30","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0048650"},{"key":"2023050608500526000_2023.05.03.539262v1.31","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-14-117"},{"key":"2023050608500526000_2023.05.03.539262v1.32","doi-asserted-by":"crossref","unstructured":"Palmieri, N. , Kosiol, C. , & Schl\u00f6tterer, C. (2014). 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C. I. , & Hamdy, F. (2017). The Drosophila Accessory Gland as a Model for Prostate Cancer and Other Pathologies. In Current Topics in Developmental Biology (pp. 339\u2013375). https:\/\/doi.org\/10.1016\/bs.ctdb.2016.06.001","DOI":"10.1016\/bs.ctdb.2016.06.001"},{"key":"2023050608500526000_2023.05.03.539262v1.45","doi-asserted-by":"publisher","DOI":"10.26508\/lsa.201800156"},{"issue":"4","key":"2023050608500526000_2023.05.03.539262v1.46","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1038\/s41559-019-0822-5","article-title":"Rapid evolution of protein diversity by de novo origination in Oryza","volume":"3","year":"2019","journal-title":"Nature Ecology & Evolution"},{"key":"2023050608500526000_2023.05.03.539262v1.47","doi-asserted-by":"publisher","DOI":"10.1126\/science.1248286"},{"key":"2023050608500526000_2023.05.03.539262v1.48","doi-asserted-by":"crossref","unstructured":"Zheng, E. B. , & Zhao, L. (2022). Protein evidence of unannotated ORFs in reveals diversity in the evolution and properties of young proteins. eLife, 11. https:\/\/doi.org\/10.7554\/eLife.78772","DOI":"10.7554\/eLife.78772"},{"issue":"3","key":"2023050608500526000_2023.05.03.539262v1.49","first-page":"215","article-title":"[A Chinese girl with fibrodysplasia ossificans progressiva caused by a de novo mutation R206H in ACVR1 gene]","volume":"46","year":"2008","journal-title":"Zhonghua er ke za zhi. Chinese journal of pediatrics"},{"key":"2023050608500526000_2023.05.03.539262v1.50","doi-asserted-by":"publisher","DOI":"10.1101\/gr.076588.108"},{"key":"2023050608500526000_2023.05.03.539262v1.51","doi-asserted-by":"crossref","unstructured":"Zhuang, X. , & Cheng, C.-H. C. (2021). Propagation of a De novo Gene under Natural Selection: Antifreeze Glycoprotein Genes and Their Evolutionary History in Codfishes. Genes, 12(11). https:\/\/doi.org\/10.3390\/genes12111777","DOI":"10.3390\/genes12111777"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2023.05.03.539262","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T04:37:17Z","timestamp":1768451837000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2023.05.03.539262"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,5,3]]},"references-count":51,"URL":"https:\/\/doi.org\/10.1101\/2023.05.03.539262","relation":{},"subject":[],"published":{"date-parts":[[2023,5,3]]},"subtype":"preprint"}}