{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T06:39:13Z","timestamp":1775284753130,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pgen.1010226","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,7,18]],"date-time":"2022-07-18T00:00:00Z","timestamp":1658102400000}}],"reference-count":114,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2022,7,6]],"date-time":"2022-07-06T00:00:00Z","timestamp":1657065600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["26073998"],"award-info":[{"award-number":["26073998"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"H2020 European Research Council","doi-asserted-by":"publisher","award":["715257"],"award-info":[{"award-number":["715257"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"abstract":"<jats:p>Polyploidization may precipitate dramatic changes to the genome, including chromosome rearrangements, gene loss, and changes in gene expression. In dioecious plants, the sex-determining mechanism may also be disrupted by polyploidization, with the potential evolution of hermaphroditism. However, while dioecy appears to have persisted through a ploidy transition in some species, it is unknown whether the newly formed polyploid maintained its sex-determining system uninterrupted, or whether dioecy re-evolved after a period of hermaphroditism. Here, we develop a bioinformatic pipeline using RNA-sequencing data from natural populations to demonstrate that the allopolyploid plant<jats:italic>Mercurialis canariensis<\/jats:italic>directly inherited its sex-determining region from one of its diploid progenitor species,<jats:italic>M<\/jats:italic>.<jats:italic>annua<\/jats:italic>, and likely remained dioecious through the transition. The sex-determining region of<jats:italic>M<\/jats:italic>.<jats:italic>canariensis<\/jats:italic>is smaller than that of its diploid progenitor, suggesting that the non-recombining region of<jats:italic>M<\/jats:italic>.<jats:italic>annua<\/jats:italic>expanded subsequent to the polyploid origin of<jats:italic>M<\/jats:italic>.<jats:italic>canariensis<\/jats:italic>. Homeologous pairs show partial sexual subfunctionalization. We discuss the possibility that gene duplicates created by polyploidization might contribute to resolving sexual antagonism.<\/jats:p>","DOI":"10.1371\/journal.pgen.1010226","type":"journal-article","created":{"date-parts":[[2022,7,6]],"date-time":"2022-07-06T17:45:15Z","timestamp":1657129515000},"page":"e1010226","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":7,"title":["Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9752-7380","authenticated-orcid":true,"given":"Melissa A.","family":"Toups","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4579-8306","authenticated-orcid":true,"given":"Beatriz","family":"Vicoso","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0098-7074","authenticated-orcid":true,"given":"John R.","family":"Pannell","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2022,7,6]]},"reference":[{"issue":"33","key":"pgen.1010226.ref001","doi-asserted-by":"crossref","first-page":"13875","DOI":"10.1073\/pnas.0811575106","article-title":"The frequency of polyploid speciation in vascular plants","volume":"106","author":"TE Wood","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"pgen.1010226.ref002","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1111\/nph.13698","article-title":"On the relative abundance of autopolyploids and allopolyploids","volume":"210","author":"MS Barker","year":"2016","journal-title":"New Phytol"},{"issue":"2","key":"pgen.1010226.ref003","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/s41559-018-0787-9","article-title":"The global biogeography of polyploid plants","volume":"3","author":"A Rice","year":"2019","journal-title":"Nat Ecol Evol"},{"issue":"1","key":"pgen.1010226.ref004","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1093\/plcell\/koaa015","article-title":"Polyploidy: an evolutionary and ecological force in stressful times","volume":"33","author":"Y Van de Peer","year":"2021","journal-title":"Plant Cell"},{"issue":"3","key":"pgen.1010226.ref005","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1002\/ajb2.1060","article-title":"Impact of whole-genome duplication events on diversification rates in angiosperms","volume":"105","author":"JB Landis","year":"2018","journal-title":"Am J Bot"},{"issue":"2","key":"pgen.1010226.ref006","doi-asserted-by":"crossref","first-page":"454","DOI":"10.1111\/nph.13491","article-title":"Nested radiations and the pulse of angiosperm diversification: Increased diversification rates often follow whole genome duplications","volume":"207","author":"DC Tank","year":"2015","journal-title":"New Phytol"},{"key":"pgen.1010226.ref007","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.pbi.2016.03.015","article-title":"Ancient WGD events as drivers of key innovations in angiosperms","volume":"30","author":"PS Soltis","year":"2016","journal-title":"Curr Opin Plant Biol"},{"issue":"2","key":"pgen.1010226.ref008","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1016\/j.pbi.2005.01.001","article-title":"Polyploidy and genome evolution in plants","volume":"8","author":"KL Adams","year":"2005","journal-title":"Curr Opin Plant Biol"},{"key":"pgen.1010226.ref009","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/j.gde.2015.11.003","article-title":"Polyploidy and genome evolution in plants","volume":"35","author":"PS Soltis","year":"2015","journal-title":"Curr Opin Genet Dev"},{"issue":"5","key":"pgen.1010226.ref010","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/35072009","article-title":"Yesterday\u2019s polyploids and the mystery of diploidization","volume":"2","author":"KH Wolfe","year":"2001","journal-title":"Nat Rev"},{"issue":"1","key":"pgen.1010226.ref011","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1111\/j.1469-8137.2009.03117.x","article-title":"Making a functional diploid: From polysomic to disomic inheritance","volume":"186","author":"SC Le Comber","year":"2010","journal-title":"New Phytol"},{"issue":"11","key":"pgen.1010226.ref012","doi-asserted-by":"crossref","first-page":"1753","DOI":"10.3732\/ajb.1500320","article-title":"The wondrous cycles of polyploidy in plants","volume":"102","author":"JF Wendel","year":"2015","journal-title":"Am J Bot"},{"issue":"7","key":"pgen.1010226.ref013","doi-asserted-by":"crossref","first-page":"934","DOI":"10.1101\/gr.4708406","article-title":"Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes","volume":"16","author":"BC Thomas","year":"2006","journal-title":"Genome Res"},{"key":"pgen.1010226.ref014","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.gde.2015.11.002","article-title":"Fractionation and subfunctionalization following genome duplications: Mechanisms that drive gene content and their consequences","volume":"35","author":"M Freeling","year":"2015","journal-title":"Curr Opin Genet Dev"},{"issue":"2","key":"pgen.1010226.ref015","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1093\/genetics\/166.2.935","article-title":"Genomic duplication, fractionation and the origin of regulatory novelty","volume":"166","author":"RJ Langham","year":"2004","journal-title":"Genetics"},{"issue":"5","key":"pgen.1010226.ref016","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1038\/s41477-018-0136-7","article-title":"Gene retention, fractionation and subgenome differences in polyploid plants","volume":"4","author":"F Cheng","year":"2018","journal-title":"Nat Plants."},{"issue":"10","key":"pgen.1010226.ref017","doi-asserted-by":"crossref","first-page":"4069","DOI":"10.1073\/pnas.1101368108","article-title":"Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss","volume":"108","author":"JC Schnable","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"pgen.1010226.ref018","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.pbi.2012.01.015","article-title":"Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants","volume":"15","author":"M Freeling","year":"2012","journal-title":"Curr Opin Plant Biol"},{"key":"pgen.1010226.ref019","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.gde.2018.01.004","article-title":"The long and short of doubling down: polyploidy, epigenetics, and the temporal dynamics of genome fractionation","volume":"49","author":"JF Wendel","year":"2018","journal-title":"Curr Opin Genet Dev"},{"key":"pgen.1010226.ref020","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1146\/annurev-genet-120213-092159","article-title":"Nonadditive gene expression in polyploids","volume":"48","author":"MJ Yoo","year":"2014","journal-title":"Annu Rev Genet"},{"issue":"4","key":"pgen.1010226.ref021","doi-asserted-by":"crossref","first-page":"1531","DOI":"10.1093\/genetics\/151.4.1531","article-title":"Preservation of duplicate genes by complementary, degenerative mutations","volume":"151","author":"A Force","year":"1999","journal-title":"Genetics"},{"issue":"1","key":"pgen.1010226.ref022","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1111\/tpj.14020","article-title":"Spatio-temporal expression dynamics differ between homologues of flowering time genes in the allopolyploid Brassica napus","volume":"96","author":"DM Jones","year":"2018","journal-title":"Plant J"},{"issue":"6403","key":"pgen.1010226.ref023","doi-asserted-by":"crossref","DOI":"10.1126\/science.aar6089","article-title":"The transcriptional landscape of polyploid wheat","volume":"361","author":"RH Ram\u00edrez-Gonz\u00e1lez","year":"2018","journal-title":"Science (80-)"},{"issue":"3","key":"pgen.1010226.ref024","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1534\/genetics.110.123729","article-title":"The resolution of sexual antagonism by gene duplication","volume":"187","author":"T Connallon","year":"2011","journal-title":"Genetics"},{"issue":"5","key":"pgen.1010226.ref025","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1016\/j.tree.2011.02.004","article-title":"Intralocus sexual conflict resolved through gene duplication","volume":"26","author":"M Gallach","year":"2011","journal-title":"Trends Ecol Evol"},{"issue":"5","key":"pgen.1010226.ref026","first-page":"1556","article-title":"Gene duplication in the evolution of sexual dimorphism","volume":"66","author":"MJ Wyman","year":"2011","journal-title":"Evolution (N Y)"},{"issue":"6","key":"pgen.1010226.ref027","doi-asserted-by":"crossref","first-page":"1581","DOI":"10.1093\/molbev\/msv049","article-title":"Sexual dimorphism and the evolution of sex-biased gene expression in the brown alga ectocarpus","volume":"32","author":"A Lipinska","year":"2015","journal-title":"Mol Biol Evol"},{"issue":"9","key":"pgen.1010226.ref028","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1002900","article-title":"A genetic basis for a postmeiotic X versus Y chromosome intragenomic conflict in the mouse","volume":"8","author":"J Cocquet","year":"2012","journal-title":"PLoS Genet."},{"issue":"1","key":"pgen.1010226.ref029","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1093\/jxb\/ers308","article-title":"Sexual dimorphism in flowering plants","volume":"64","author":"SCH Barrett","year":"2013","journal-title":"J Exp Bot"},{"key":"pgen.1010226.ref030","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1159\/000353306","article-title":"Revisiting the dioecy-polyploidy association: alternate pathways and research opportunities","volume":"140","author":"T-L Ashman","year":"2013","journal-title":"Cytogenet Genome Res"},{"issue":"4","key":"pgen.1010226.ref031","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1111\/j.1095-8312.2004.00340.x","article-title":"Polyploidy and the sexual system: What can we learn from Mercurialis annua?","volume":"82","author":"JR Pannell","year":"2004","journal-title":"Biol J Linn Soc"},{"key":"pgen.1010226.ref032","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1159\/000351998","article-title":"Polyploidy in animals: Effects of gene expression on sex determination, evolution and ecology","volume":"140","author":"B Wertheim","year":"2013","journal-title":"Cytogenet Genome Res"},{"key":"pgen.1010226.ref033","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1111\/nph.13499","article-title":"Meiosis evolves: Adaptation to external and internal environments","volume":"208","author":"K Bomblies","year":"2015","journal-title":"New Phytol"},{"key":"pgen.1010226.ref034","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/S0065-2660(08)60163-7","article-title":"The mechanism of sex determination in dioecious flowering plants","volume":"9","author":"M. Westergaard","year":"1958","journal-title":"Adv Genet"},{"issue":"1","key":"pgen.1010226.ref035","doi-asserted-by":"crossref","first-page":"605","DOI":"10.5642\/aliso.20072301.45","article-title":"Dicliny in Bouteloua (Poaceae: Chloridoideae): Implications for the Evolution of Dioecy","volume":"23","author":"M Kinney","year":"2007","journal-title":"Aliso"},{"issue":"8","key":"pgen.1010226.ref036","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1007\/BF00277336","article-title":"The mechanism of sex determination in Rumex acetosella","volume":"41","author":"RB Singh","year":"1971","journal-title":"Theor Appl Genet"},{"issue":"6","key":"pgen.1010226.ref037","doi-asserted-by":"crossref","first-page":"673","DOI":"10.2307\/2440524","article-title":"Cytogeography and Cytotaxonomic Relationships of Rumex paucifolius","volume":"55","author":"BENW Smith","year":"1968","journal-title":"Am J Bot"},{"key":"pgen.1010226.ref038","doi-asserted-by":"crossref","first-page":"555","DOI":"10.3732\/ajb.1400494","article-title":"Hybridization is associated with changes in sexual system in the bryophyte genus Atrichum","volume":"102","author":"DS Perley","year":"2015","journal-title":"Am J Bot"},{"key":"pgen.1010226.ref039","doi-asserted-by":"crossref","first-page":"20200089","DOI":"10.1098\/rstb.2020.0089","article-title":"A 180 Myr-old female-specific genome region in sturgeon reveals the oldest known vertebrate sex determining system with undifferentiated sex chromosomes","volume":"376","author":"H Kuhl","year":"2021","journal-title":"Proc R Soc B Biol Sci"},{"key":"pgen.1010226.ref040","doi-asserted-by":"crossref","first-page":"eabh2488","DOI":"10.1126\/sciadv.abh2488","article-title":"Gene-rich UV sex chromosomes harbor conserved regulators of sexual development","volume":"7","author":"SB Carey","year":"2021","journal-title":"Sci Adv"},{"issue":"5488","key":"pgen.1010226.ref041","doi-asserted-by":"crossref","first-page":"2335","DOI":"10.1126\/science.289.5488.2335","article-title":"Polyploidy and the evolution of gender dimorphism in plants","volume":"289","author":"JS Miller","year":"2000","journal-title":"Science (80-)"},{"issue":"8","key":"pgen.1010226.ref042","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pbio.2006062","article-title":"Repeated translocation of a gene cassette drives sex-chromosome turnover in strawberries","volume":"16","author":"JA Tennessen","year":"2018","journal-title":"PLoS Biol"},{"issue":"1","key":"pgen.1010226.ref043","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1111\/nph.14711","article-title":"Present-day sympatry belies the evolutionary origin of a high-order polyploid","volume":"216","author":"N Wei","year":"2017","journal-title":"New Phytol"},{"issue":"10","key":"pgen.1010226.ref044","doi-asserted-by":"crossref","first-page":"1686","DOI":"10.3732\/ajb.1400140","article-title":"Fragaria: A genus with deep historical roots and ripe for evolutionary and ecological insights","volume":"101","author":"A Liston","year":"2014","journal-title":"Am J Bot"},{"issue":"4","key":"pgen.1010226.ref045","doi-asserted-by":"crossref","first-page":"1412","DOI":"10.1111\/nph.13983","article-title":"Homomorphic ZW chromosomes in a wild strawberry show distinctive recombination heterogeneity but a small sex-determining region","volume":"211","author":"JA Tennessen","year":"2016","journal-title":"New Phytol"},{"issue":"4","key":"pgen.1010226.ref046","first-page":"1114","article-title":"Genetic architecture of sexual dimorphism in a subdioecious plant with a proto-sex chromosome","volume":"65","author":"RB Spigler","year":"2011","journal-title":"Evolution (N Y)"},{"issue":"7","key":"pgen.1010226.ref047","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1093\/jhered\/esx077","article-title":"Genetic mapping and phylogenetic analysis reveal intraspecific variation in sex chromosomes of the Virginian strawberry","volume":"108","author":"N Wei","year":"2017","journal-title":"J Hered"},{"key":"pgen.1010226.ref048","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1093\/jhered\/esq001","article-title":"Comparative mapping reveals autosomal origin of sex chromosome in octoploid Fragaria virginiana","volume":"101","author":"RB Spigler","year":"2010","journal-title":"J Hered"},{"issue":"6","key":"pgen.1010226.ref049","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1038\/hdy.2008.100","article-title":"Genetic mapping of sex determination in a wild strawberry, Fragaria virginiana, reveals earliest form of sex chromosome","volume":"101","author":"RB Spigler","year":"2008","journal-title":"Heredity (Edinb)"},{"issue":"12","key":"pgen.1010226.ref050","doi-asserted-by":"crossref","first-page":"3295","DOI":"10.1093\/gbe\/evu261","article-title":"Evolutionary origins and dynamics of octoploid strawberry subgenomes revealed by dense targeted capture linkage maps","volume":"6","author":"JA Tennessen","year":"2014","journal-title":"Genome Biol Evol"},{"issue":"2","key":"pgen.1010226.ref051","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pgen.1008566","article-title":"The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants","volume":"16","author":"T Akagi","year":"2020","journal-title":"PLoS Genet"},{"issue":"6209","key":"pgen.1010226.ref052","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1126\/science.1257225","article-title":"A Y-chromosome\u2013encoded small RNA acts as a sex determinant in persimmons","volume":"346","author":"T Akagi","year":"2014","journal-title":"Science (80-)"},{"issue":"12","key":"pgen.1010226.ref053","first-page":"1","article-title":"Molecular mechanism underlying derepressed male production in hexaploid persimmon","volume":"11","author":"K Masuda","year":"2020","journal-title":"Front Plant Sci"},{"key":"pgen.1010226.ref054","first-page":"579","article-title":"Le complexe Mercurialis annua L. s.l. une \u00e9tude biosyst\u00e9matique","volume":"12","author":"B. Durand","year":"1963","journal-title":"Ann des Sci Nat Bot Paris"},{"issue":"9","key":"pgen.1010226.ref055","first-page":"1801","article-title":"Hybridization, polyploidy, and the evolution of sexual systems in Mercurialis (Euphorbiaceae)","volume":"60","author":"DJ Obbard","year":"2006","journal-title":"Evolution (N Y)"},{"issue":"3","key":"pgen.1010226.ref056","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1038\/hdy.2014.95","article-title":"Sex determination in dioecious Mercurialis annua and its close diploid and polyploid relatives","volume":"114","author":"JRW Russell","year":"2015","journal-title":"Heredity (Edinb)"},{"issue":"1","key":"pgen.1010226.ref057","first-page":"99","article-title":"Mercurialis canariensis (Euphorbiaceae), a new endemic to the Canary Islands","volume":"61","author":"DJ Obbard","year":"2006","journal-title":"Kew Bull"},{"key":"pgen.1010226.ref058","article-title":"The maintenance of dioecy and chromosomal sex determination through allopolyploid speciation in the plant genus Mercurialis.","author":"MA Toups","year":"2022","journal-title":"Dryad, Dataset"},{"key":"pgen.1010226.ref059","article-title":"The maintenance of dioecy and chromosomal sex determination through allopolyploid speciation in the plant genus Mercurialis","author":"MA Toups","year":"2022","journal-title":"Zenodo, Softw"},{"issue":"7","key":"pgen.1010226.ref060","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1534\/genetics.119.302045","article-title":"Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua","volume":"212","author":"P Veltsos","year":"2019","journal-title":"Genetics"},{"issue":"6","key":"pgen.1010226.ref061","doi-asserted-by":"crossref","first-page":"738","DOI":"10.1101\/gr.4825606","article-title":"Widespread genome duplications throughout the history of flowering plants","volume":"16","author":"L Cui","year":"2006","journal-title":"Genome Res"},{"issue":"7","key":"pgen.1010226.ref062","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1093\/aob\/mcy183","article-title":"Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb","volume":"123","author":"GG Cossard","year":"2019","journal-title":"Ann Bot"},{"key":"pgen.1010226.ref063","article-title":"limma powers differential expression analyses for","volume":"43","author":"ME Ritchie","year":"2015","journal-title":"RNA-sequencing and microarray studies"},{"issue":"1","key":"pgen.1010226.ref064","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1111\/j.1469-8137.2009.03107.x","article-title":"Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation","volume":"186","author":"LE Flagel","year":"2010","journal-title":"New Phytol"},{"key":"pgen.1010226.ref065","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1016\/j.pbi.2020.03.004","article-title":"One subgenome to rule them all: underlying mechanisms of subgenome dominance","volume":"54","author":"EI Alger","year":"2020","journal-title":"Curr Opin Plant Biol"},{"issue":"1","key":"pgen.1010226.ref066","first-page":"1","article-title":"The allotetraploid origin and asymmetrical genome evolution of the common carp Cyprinus carpio","volume":"10","author":"P Xu","year":"2019","journal-title":"Nat Commun"},{"issue":"9","key":"pgen.1010226.ref067","doi-asserted-by":"crossref","first-page":"2150","DOI":"10.1105\/tpc.17.00010","article-title":"Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140-year-old naturally established neo-allopolyploid monkeyflower","volume":"29","author":"PP Edger","year":"2017","journal-title":"Plant Cell"},{"issue":"19","key":"pgen.1010226.ref068","doi-asserted-by":"crossref","first-page":"1293","DOI":"10.1016\/j.molp.2017.09.003","article-title":"Karyotype stability and unbiased fractionation in the paleo-allotetraploid Cucurbita genomes","volume":"10","author":"H Sun","year":"2017","journal-title":"Mol Plant"},{"issue":"3","key":"pgen.1010226.ref069","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/gigascience\/giz012","article-title":"Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry","volume":"8","author":"M Colle","year":"2019","journal-title":"Gigascience"},{"key":"pgen.1010226.ref070","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12870-014-0276-5","article-title":"Populus tremula (European aspen) shows no evidence of sexual dimorphism","volume":"14","author":"KM Robinson","year":"2014","journal-title":"BMC Plant Biol"},{"issue":"1","key":"pgen.1010226.ref071","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1111\/nph.15421","article-title":"Sex-biased gene expression in flowers, but not leaves, reveals secondary sexual dimorphism in Populus balsamifera","volume":"221","author":"BJ Sanderson","year":"2019","journal-title":"New Phytol"},{"issue":"3","key":"pgen.1010226.ref072","doi-asserted-by":"crossref","first-page":"694","DOI":"10.1111\/mec.14466","article-title":"Slow evolution of sex-biased genes in the reproductive tissue of the dioecious plant Salix viminalis","volume":"27","author":"I Darolti","year":"2018","journal-title":"Mol Ecol"},{"issue":"3","key":"pgen.1010226.ref073","doi-asserted-by":"crossref","first-page":"883","DOI":"10.1111\/nph.13389","article-title":"Sex-biased gene expression in dioecious garden asparagus (Asparagus officinalis)","volume":"207","author":"A Harkess","year":"2015","journal-title":"New Phytol"},{"issue":"11","key":"pgen.1010226.ref074","doi-asserted-by":"crossref","DOI":"10.1038\/nplants.2016.168","article-title":"Evolution of sex-biased gene expression in a dioecious plant","volume":"2(","author":"N Zemp","year":"2016","journal-title":"Nat Plants"},{"key":"pgen.1010226.ref075","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1101\/gr.251207.119","article-title":"An efficient RNA-seq-based segregation analysis identifies the sex chromosomes of Cannabis sativa","volume":"30","author":"D Prentout","year":"2020","journal-title":"Genome Res"},{"key":"pgen.1010226.ref076","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1146\/annurev-genet-120215-035429","article-title":"Sex-Biased Gene Expression","volume":"50","author":"S Grath","year":"2016","journal-title":"Annu Rev Genet"},{"issue":"3","key":"pgen.1010226.ref077","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1093\/gbe\/evw282","article-title":"The evolution of sex chromosomes and dosage compensation in plants","volume":"9","author":"A Muyle","year":"2017","journal-title":"Genome Biol Evol"},{"issue":"7","key":"pgen.1010226.ref078","doi-asserted-by":"crossref","first-page":"IV","DOI":"10.1093\/aob\/mcz081","article-title":"How different is the evolution of sex-biased gene expression between plants and animals? A commentary on: \u201cSexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb.\u201d","volume":"123","author":"A. Muyle","year":"2019","journal-title":"Ann Bot"},{"issue":"1","key":"pgen.1010226.ref079","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1093\/aob\/mcz058","article-title":"A new biological species in the Mercurialis annua polyploid complex: Functional divergence in inflorescence morphology and hybrid sterility","volume":"124","author":"WJ Ma","year":"2019","journal-title":"Ann Bot"},{"issue":"1","key":"pgen.1010226.ref080","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-020-17302-5","article-title":"Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors","volume":"11","author":"SP Gordon","year":"2020","journal-title":"Nat Commun"},{"issue":"9","key":"pgen.1010226.ref081","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1016\/S0169-5347(99)01638-9","article-title":"Polyploidy: Recurrent formation and genome evolution","volume":"14","author":"DE Soltis","year":"1999","journal-title":"Trends Ecol Evol"},{"issue":"5","key":"pgen.1010226.ref082","doi-asserted-by":"crossref","first-page":"1695","DOI":"10.1093\/molbev\/msaa327","article-title":"Linked by ancestral bonds: Multiple whole-genome duplications and reticulate evolution in a Brassicaceae tribe","volume":"38","author":"X Guo","year":"2021","journal-title":"Mol Biol Evol"},{"issue":"4","key":"pgen.1010226.ref083","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1111\/j.1095-8312.2004.00335.x","article-title":"Recent and recurrent polyploidy in Tragopogon (Asteraceae): Cytogenetic, genomic and genetic comparisons","volume":"82","author":"DE Soltis","year":"2004","journal-title":"Biol J Linn Soc"},{"issue":"7","key":"pgen.1010226.ref084","doi-asserted-by":"crossref","first-page":"1467","DOI":"10.1111\/jeb.12352","article-title":"Regional variation in sex ratios and sex allocation in androdioecious Mercurialis annua","volume":"27","author":"JR Pannell","year":"2014","journal-title":"J Evol Biol"},{"key":"pgen.1010226.ref085","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3389\/fevo.2018.00117","article-title":"The \u201cPolyploid Hop\u201d: Shifting challenges and opportunities over the evolutionary lifespan of genome duplications.","volume":"6","author":"P Baduel","year":"2018","journal-title":"Front Ecol Evol"},{"key":"pgen.1010226.ref086","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1111\/nph.13539","article-title":"The scope of Baker\u2019s law","volume":"208","author":"JR Pannell","year":"2015","journal-title":"New Phytol"},{"issue":"1","key":"pgen.1010226.ref087","doi-asserted-by":"crossref","first-page":"244","DOI":"10.2307\/2399068","article-title":"Further thoughts on dioecism and islands","volume":"71","author":"HG Baker","year":"1984","journal-title":"Ann Missouri Bot Gard"},{"issue":"8","key":"pgen.1010226.ref088","doi-asserted-by":"crossref","first-page":"2517","DOI":"10.2307\/2265825","article-title":"Origins of dioecy in the Hawaiian flora","volume":"76","author":"AK Sakai","year":"1995","journal-title":"Ecology"},{"issue":"1","key":"pgen.1010226.ref089","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1080\/0028825X.1999.9512618","article-title":"Gender dimorphism in indigenous New Zealand seed plants","volume":"37","author":"CJ Webb","year":"1999","journal-title":"New Zeal J Bot"},{"key":"pgen.1010226.ref090","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1098\/rstb.1996.0067","article-title":"The reproductive biology and genetics of island plants","volume":"351","author":"SCH Barrett","year":"1996","journal-title":"Philos Trans R Soc B Biol Sci"},{"issue":"4","key":"pgen.1010226.ref091","doi-asserted-by":"crossref","first-page":"310","DOI":"10.2307\/2805148","article-title":"The biota of long-distance dispersal. III. Loss of dispersibility in the Hawaiian flora","volume":"18","author":"S. Carlquist","year":"1966","journal-title":"Brittonia"},{"issue":"3","key":"pgen.1010226.ref092","first-page":"347","article-title":"Self-compatibility and establishment after \u201clong-distance\u201d dispersal.","volume":"9","author":"HG Baker","year":"1955","journal-title":"Evolution (N Y)."},{"issue":"4","key":"pgen.1010226.ref093","first-page":"853","article-title":"Support for Baker\u2019s Law\u2014as a rule","volume":"21","author":"HG Baker","year":"1967","journal-title":"Evolution (N Y)."},{"issue":"2","key":"pgen.1010226.ref094","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1111\/jeb.13720","article-title":"Enhanced leaky sex expression in response to pollen limitation in the dioecious plant Mercurialis annua","volume":"34","author":"GG Cossard","year":"2021","journal-title":"J Evol Biol"},{"key":"pgen.1010226.ref095","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1002\/ajb2.1277","article-title":"A functional decomposition of sex inconstancy in the dioecious, colonizing plant Mercurialis annua","volume":"106","author":"GG Cossard","year":"2019","journal-title":"Am J Bot"},{"issue":"8","key":"pgen.1010226.ref096","first-page":"1","article-title":"De novo transcript sequence recostruction from RNA-Seq: reference generation and analysis with Trinity","volume":"8","author":"BJ Haas","year":"2013","journal-title":"Nat Protoc"},{"issue":"15","key":"pgen.1010226.ref097","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 Bolger","year":"2014","journal-title":"Bioinformatics"},{"issue":"9","key":"pgen.1010226.ref098","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"A. Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"issue":"5","key":"pgen.1010226.ref099","first-page":"1","article-title":"-a command line software package for phylogenetics","volume":"2903","author":"Ryberg M. Phylommand","year":"2019","journal-title":"F1000Research"},{"issue":"10","key":"pgen.1010226.ref100","doi-asserted-by":"crossref","first-page":"1372","DOI":"10.1093\/bioinformatics\/btq110","article-title":"DensiTree: Making sense of sets of phylogenetic trees","volume":"26","author":"RR Bouckaert","year":"2010","journal-title":"Bioinformatics"},{"issue":"6","key":"pgen.1010226.ref101","first-page":"1358","article-title":"Estimating F-statistics for the analysis of population structure","volume":"38","author":"BS Weir","year":"1984","journal-title":"Evolution (N Y)."},{"issue":"6","key":"pgen.1010226.ref102","doi-asserted-by":"crossref","first-page":"1517","DOI":"10.1111\/1755-0998.13210","article-title":"Disagreement in FST estimators: A case study from sex chromosomes","volume":"20","author":"WJ Gammerdinger","year":"2020","journal-title":"Mol Ecol Resour"},{"key":"pgen.1010226.ref103","article-title":"Using conventional F-statistics to study unconventional sex-chromosome differentiation","volume":"4","author":"N Rodrigues","year":"2017","journal-title":"PeerJ"},{"issue":"1","key":"pgen.1010226.ref104","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: Ultrafast universal RNA-seq aligner","volume":"29","author":"A Dobin","year":"2013","journal-title":"Bioinformatics"},{"issue":"16","key":"pgen.1010226.ref105","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"17","key":"pgen.1010226.ref106","doi-asserted-by":"crossref","first-page":"2283","DOI":"10.1093\/bioinformatics\/btp373","article-title":"VarScan: Variant detection in massively parallel sequencing of individual and pooled samples","volume":"25","author":"DC Koboldt","year":"2009","journal-title":"Bioinformatics"},{"issue":"15","key":"pgen.1010226.ref107","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"P Danecek","year":"2011","journal-title":"Bioinformatics"},{"issue":"8","key":"pgen.1010226.ref108","doi-asserted-by":"crossref","first-page":"1877","DOI":"10.1111\/mec.14990","article-title":"A reciprocal translocation radically reshapes sex-linked inheritance in the common frog","volume":"28","author":"MA Toups","year":"2019","journal-title":"Mol Ecol"},{"issue":"5","key":"pgen.1010226.ref109","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nbt.3519","article-title":"Near-optimal probabilistic RNA-seq quantification","volume":"34","author":"NL Bray","year":"2016","journal-title":"Nat Biotechnol"},{"issue":"2","key":"pgen.1010226.ref110","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.12688\/f1000research.7563.1","article-title":"Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences","volume":"4","author":"C Soneson","year":"2015","journal-title":"F1000Research"},{"issue":"12","key":"pgen.1010226.ref111","first-page":"1","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"MI Love","year":"2014","journal-title":"Genome Biol"},{"issue":"1","key":"pgen.1010226.ref112","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: A practical and powerful approach to multiple testing","volume":"57","author":"Y Benjamini","year":"1995","journal-title":"J R Stat Soc Ser B"},{"issue":"4","key":"pgen.1010226.ref113","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1003457","article-title":"Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap","volume":"9","author":"P Gayral","year":"2013","journal-title":"PLoS Genet"},{"key":"pgen.1010226.ref114","doi-asserted-by":"crossref","DOI":"10.3389\/fpls.2020.01056","article-title":"Chromosome Pairing in Polyploid Grasses.","volume":"11","author":"R Sva\u010dina","year":"2020","journal-title":"Front Plant Sci"}],"updated-by":[{"DOI":"10.1371\/journal.pgen.1010226","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,7,18]],"date-time":"2022-07-18T00:00:00Z","timestamp":1658102400000}}],"container-title":["PLOS Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1010226","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,28]],"date-time":"2024-09-28T16:44:08Z","timestamp":1727541848000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1010226"}},"subtitle":[],"editor":[{"given":"Tanja","family":"Slotte","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2022,7,6]]},"references-count":114,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2022,7,6]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1010226","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pgen.1010226","asserted-by":"object"}]},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,7,6]]}}}