{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:12:56Z","timestamp":1790813576165,"version":"4.1.0"},"update-to":[{"DOI":"10.1371\/journal.ppat.1013282","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T00:00:00Z","timestamp":1754006400000}}],"reference-count":44,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2025,7,23]],"date-time":"2025-07-23T00:00:00Z","timestamp":1753228800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100015691","name":"Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R21AI149449"],"award-info":[{"award-number":["R21AI149449"]}],"id":[{"id":"10.13039\/100015691","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>\n                    <jats:italic>Trichomonas vaginalis<\/jats:italic>\n                    infects the urogenital tract of men and women and causes the sexually transmitted infection trichomoniasis. Since the publication of its draft genome in 2007, the genome has drawn attention for several reasons, including its unusually large size, massive expansion of gene families, and high repeat content. The fragmented nature of the draft assembly made it challenging to obtain accurate metrics of features, such as spliceosomal introns. The number of introns identified has varied over the years, ranging from 41 when first characterized in 2005, to 32 in 2018 when the repertoire was revised. In both cases, the results suggested that more introns could be present in the genome. In this study, we exploited our new\n                    <jats:italic>T. vaginalis<\/jats:italic>\n                    G3 chromosome-scale assembly and annotation and high-coverage transcriptome datasets to provide an up-to-date repertoire of spliceosomal introns in the species. We developed a custom pipeline that distinguishes true splicing events from chimeric alignments by utilizing the extended motifs required by the splicing machinery, and experimentally verified the results using transcript evidence. We identified a total of 63 active introns and 34 putative \u201cinactive\u201d intron sequences in\n                    <jats:italic>T. vaginalis<\/jats:italic>\n                    , enabling an analysis of their length distribution, extended consensus motifs, intron phase distribution (including an unexpected expansion of UTR introns), and functional annotation. Notably, we found that a short intron in\n                    <jats:italic>T. vaginalis<\/jats:italic>\n                    , at only 23 nucleotides in size, is one of the shortest introns known to date. We tested our pipeline on a chromosome-scale assembly of the bird parasite\n                    <jats:italic>Trichomonas stableri<\/jats:italic>\n                    , the closest known relative to\n                    <jats:italic>T. vaginalis<\/jats:italic>\n                    . Our results revealed some conservation of the main features (total intron count, sequence, length distribution, and motifs) of these two closely related species, although differences in their functional annotation and duplication suggest alternative splicing machinery in\n                    <jats:italic>T. vaginalis<\/jats:italic>\n                    .\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1013282","type":"journal-article","created":{"date-parts":[[2025,7,23]],"date-time":"2025-07-23T17:44:23Z","timestamp":1753292663000},"page":"e1013282","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":6,"title":["Redefining the spliceosomal introns of the sexually transmitted parasite Trichomonas vaginalis and its close relative in columbid birds"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2378-3904","authenticated-orcid":true,"given":"Francisco","family":"Callejas-Hern\u00e1ndez","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mari","family":"Shiratori","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven A.","family":"Sullivan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frances","family":"Blow","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9340-5020","authenticated-orcid":true,"given":"Jane M.","family":"Carlton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,7,23]]},"reference":[{"key":"ppat.1013282.ref001","doi-asserted-by":"crossref","first-page":"851635","DOI":"10.3389\/fmed.2022.851635","article-title":"Incidence trends of five common sexually transmitted infections excluding HIV from 1990 to 2019 at the global, regional, and national levels: results from the Global Burden of Disease Study 2019","volume":"9","author":"L Fu","year":"2022","journal-title":"Front Med (Lausanne)"},{"key":"ppat.1013282.ref002","unstructured":"CDC. Trichomoniasis, Center for Disease Control and Prevention 2023. Available from: https:\/\/www.cdc.gov\/std\/treatment-guidelines\/trichomoniasis.htm"},{"issue":"5","key":"ppat.1013282.ref003","doi-asserted-by":"crossref","first-page":"698","DOI":"10.1086\/511278","article-title":"Infection with Trichomonas vaginalis increases the risk of HIV-1 acquisition","volume":"195","author":"RS McClelland","year":"2007","journal-title":"J Infect Dis"},{"issue":"2","key":"ppat.1013282.ref004","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1093\/cid\/ciy085","article-title":"Why does Trichomonas vaginalis continue to be a \u201cNeglected\u201d sexually transmitted infection?","volume":"67","author":"CA Muzny","year":"2018","journal-title":"Clin Infect Dis"},{"issue":"1","key":"ppat.1013282.ref005","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1016\/j.ijppaw.2013.12.002","article-title":"Trichomonas stableri n. sp., an agent of trichomonosis in Pacific Coast band-tailed pigeons (Patagioenas fasciata monilis)","volume":"3","author":"YA Girard","year":"2013","journal-title":"Int J Parasitol Parasites Wildl"},{"issue":"6","key":"ppat.1013282.ref006","doi-asserted-by":"crossref","first-page":"1335","DOI":"10.1645\/GE-1585.1","article-title":"Molecular characterization of the Trichomonas gallinae morphologic complex in the United States","volume":"94","author":"RW Gerhold","year":"2008","journal-title":"J Parasitol"},{"key":"ppat.1013282.ref007","doi-asserted-by":"crossref","first-page":"106674","DOI":"10.1016\/j.ympev.2019.106674","article-title":"Diverse Trichomonas lineages in Australasian pigeons and doves support a columbid origin for the genus Trichomonas","volume":"143","author":"A Peters","year":"2020","journal-title":"Mol Phylogenet Evol"},{"issue":"5809","key":"ppat.1013282.ref008","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1126\/science.1132894","article-title":"Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis","volume":"315","author":"JM Carlton","year":"2007","journal-title":"Science"},{"issue":"7","key":"ppat.1013282.ref009","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1134\/S0006297920070019","article-title":"Spliceosomal introns: features, functions, and evolution","volume":"85","author":"IV Poverennaya","year":"2020","journal-title":"Biochemistry (Mosc)"},{"key":"ppat.1013282.ref010","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/1745-6150-7-11","article-title":"Origin and evolution of spliceosomal introns","volume":"7","author":"IB Rogozin","year":"2012","journal-title":"Biol Direct"},{"issue":"1","key":"ppat.1013282.ref011","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1186\/s13071-018-3196-7","article-title":"Spliceosomal introns in Trichomonas vaginalis revisited","volume":"11","author":"SE Wang","year":"2018","journal-title":"Parasit Vectors"},{"issue":"12","key":"ppat.1013282.ref012","doi-asserted-by":"crossref","first-page":"4430","DOI":"10.1073\/pnas.0407500102","article-title":"Spliceosomal introns in the deep-branching eukaryote Trichomonas vaginalis","volume":"102","author":"S Van\u00e1cov\u00e1","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"ppat.1013282.ref013","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.biocel.2008.09.014","article-title":"A 25-bp ancient spliceosomal intron in the TvRab1a gene of Trichomonas vaginalis","volume":"41","author":"X-L Deng","year":"2009","journal-title":"Int J Biochem Cell Biol"},{"key":"ppat.1013282.ref014","doi-asserted-by":"crossref","first-page":"6487","DOI":"10.1038\/s41467-025-61483-w","article-title":"Comparative genomics of the parasite Trichomonas vaginalis reveals genes involved in spillover from birds to humans","volume":"16","author":"SA Sullivan","year":"2025","journal-title":"Nat Commun."},{"issue":"12","key":"ppat.1013282.ref015","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1038\/s41576-020-0251-y","article-title":"Measuring and interpreting transposable element expression","volume":"21","author":"S Lanciano","year":"2020","journal-title":"Nat Rev Genet"},{"key":"ppat.1013282.ref016","article-title":"Quality assessment of splice site annotation based on conservation across multiple species","author":"I Minkin","year":"2023","journal-title":"bioRxiv"},{"key":"ppat.1013282.ref017","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1016\/j.meegid.2014.03.002","article-title":"Dual-pathogen etiology of avian trichomonosis in a declining band-tailed pigeon population","volume":"24","author":"YA Girard","year":"2014","journal-title":"Infect Genet Evol"},{"issue":"1","key":"ppat.1013282.ref018","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1186\/s12862-019-1488-y","article-title":"Patterns of conservation of spliceosomal intron 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small nucleolar RNA is processed from an intron of the human gene encoding ribosomal protein S3","volume":"7","author":"KT Tycowski","year":"1993","journal-title":"Genes Dev"},{"issue":"6","key":"ppat.1013282.ref029","doi-asserted-by":"crossref","first-page":"2357","DOI":"10.1093\/nar\/gkq1080","article-title":"Critical association of ncRNA with introns","volume":"39","author":"D Rearick","year":"2011","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"ppat.1013282.ref030","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1016\/j.pt.2023.09.009","article-title":"Persistent Trichomonas vaginalis infections and the pseudocyst form","volume":"39","author":"M Shiratori","year":"2023","journal-title":"Trends Parasitol"},{"issue":"4","key":"ppat.1013282.ref031","doi-asserted-by":"crossref","first-page":"488","DOI":"10.2307\/3274682","article-title":"The establishment of various trichomonads of animals and man in axenic cultures","volume":"43","author":"LS Diamond","year":"1957","journal-title":"J Parasitol"},{"issue":"1","key":"ppat.1013282.ref032","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.molbiopara.2010.08.006","article-title":"Microsatellite polymorphism in the sexually transmitted human pathogen Trichomonas vaginalis indicates a genetically diverse parasite","volume":"175","author":"M Conrad","year":"2011","journal-title":"Mol Biochem Parasitol"},{"key":"ppat.1013282.ref033","volume-title":"FastQC: a quality control tool for high throughput sequence data","author":"S Andrews","year":"2010"},{"issue":"15","key":"ppat.1013282.ref034","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"AM 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native and syntenically mapped cDNA alignments to improve de novo gene finding","volume":"24","author":"M Stanke","year":"2008","journal-title":"Bioinformatics"},{"key":"ppat.1013282.ref039","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gki442","article-title":"InterProScan: protein domains identifier","volume":"33","author":"E Quevillon","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ppat.1013282.ref040","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkac240","article-title":"Search and sequence analysis tools services from EMBL-EBI in 2022","volume":"50","author":"F Madeira","year":"2022","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"ppat.1013282.ref041","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1093\/bioinformatics\/btp033","article-title":"Jalview Version 2--a multiple sequence alignment editor and analysis workbench","volume":"25","author":"AM Waterhouse","year":"2009","journal-title":"Bioinformatics"},{"issue":"1","key":"ppat.1013282.ref042","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"JT Robinson","year":"2011","journal-title":"Nat Biotechnol"},{"issue":"6","key":"ppat.1013282.ref043","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"WebLogo: a sequence logo generator","volume":"14","author":"GE Crooks","year":"2004","journal-title":"Genome Res"},{"key":"ppat.1013282.ref044","unstructured":"Team RC. 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