{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T16:59:14Z","timestamp":1791824354349,"version":"4.3.4"},"update-to":[{"DOI":"10.1371\/journal.pgen.1012241","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,7,31]],"date-time":"2026-07-31T00:00:00Z","timestamp":1785456000000}}],"reference-count":96,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T00:00:00Z","timestamp":1784851200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/S014896\/1"],"award-info":[{"award-number":["BB\/S014896\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/P02307X\/1"],"award-info":[{"award-number":["BB\/P02307X\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"abstract":"<jats:p>\n                    The high incidence of polyploidy in crops could be explained if domestication involved the selection of polyploids (cytotypes with more than two sets of chromosomes). Ancestral horticulture could have targeted desirable traits including yield, robustness to stress or disease, rather than requiring knowledge of polyploidy itself. We find evidence for this process underway in enset (\n                    <jats:italic>Ensete ventricosum<\/jats:italic>\n                    , Musaceae), a highly resilient crop constituting the main staple for over 20 million people in Ethiopia, which is clonally propagated and cultivated for its starch-rich corm and pseudostem. Prior to this study, enset was thought to be exclusively diploid (2n\u2009=\u20092x\u2009=\u200918). Using a newly-assembled chromosome-scale reference genome and sequence data from 723 wild and domesticated enset individuals from southwestern Ethiopia, we demonstrate that around 20% of cultivated enset clones are triploid. We show that triploidy has arisen multiple times independently, that the triploid lineages have been given distinct landrace names, and planted disproportionately frequently. Enset triploid clones also have a higher pseudostem volume than diploids on average. As well as providing evidence for enduring selection on triploids, our results reveal valuable genetic diversity captured by these triploid lines. They represent key resources for scientifically directed breeding of this major crop in the Ethiopian agrosystem, and could improve food security in Sub-Saharan Africa.\n                  <\/jats:p>","DOI":"10.1371\/journal.pgen.1012241","type":"journal-article","created":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T17:44:49Z","timestamp":1784915089000},"page":"e1012241","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":2,"title":["Recurrent evolution of cryptic triploids in cultivated enset increases yield"],"prefix":"10.1371","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1900-7715","authenticated-orcid":true,"given":"Yann","family":"Dussert","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James S.","family":"Borrell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan","family":"Stocks","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0075-6660","authenticated-orcid":true,"given":"Harriet V.","family":"Hunt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6444-0310","authenticated-orcid":true,"given":"Oliver W.","family":"White","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Wilkin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Buggs","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1935-6176","authenticated-orcid":true,"given":"Lucie","family":"B\u00fcchi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0123-9596","authenticated-orcid":true,"given":"Sebsebe","family":"Demissew","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feleke","family":"Woldeyes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ilia J.","family":"Leitch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wendawek M.","family":"Abebe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4801-9312","authenticated-orcid":true,"given":"Richard A.","family":"Nichols","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,7,24]]},"reference":[{"issue":"1","key":"pgen.1012241.ref001","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/aob\/mcac132","article-title":"Polyploidy: its consequences and enabling role in plant diversification and evolution","volume":"131","author":"JSP Heslop-Harrison","year":"2023","journal-title":"Ann Bot"},{"issue":"3","key":"pgen.1012241.ref002","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"},{"key":"pgen.1012241.ref003","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1038\/s41586-019-1693-2","article-title":"One thousand plant transcriptomes and the phylogenomics of green plants","volume":"574","author":"JH Leebens-Mack","year":"2019","journal-title":"Nature"},{"key":"pgen.1012241.ref004","doi-asserted-by":"crossref","first-page":"16115","DOI":"10.1038\/nplants.2016.115","article-title":"Whole-genome duplication as a key factor in crop domestication","volume":"2","author":"A Salman-Minkov","year":"2016","journal-title":"Nat Plants"},{"key":"pgen.1012241.ref005","doi-asserted-by":"crossref","first-page":"102255","DOI":"10.1016\/j.pbi.2022.102255","article-title":"Polyploidy before and after domestication of crop species","volume":"69","author":"T Akagi","year":"2022","journal-title":"Curr Opin Plant Biol"},{"issue":"3","key":"pgen.1012241.ref006","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1016\/j.cell.2007.10.022","article-title":"The evolutionary consequences of polyploidy","volume":"131","author":"SP Otto","year":"2007","journal-title":"Cell"},{"issue":"1","key":"pgen.1012241.ref007","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1093\/aob\/mcr277","article-title":"The more the better? The role of polyploidy in facilitating plant invasions","volume":"109","author":"M te Beest","year":"2012","journal-title":"Ann Bot"},{"issue":"1","key":"pgen.1012241.ref008","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":"1","key":"pgen.1012241.ref009","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1111\/j.1469-8137.2012.04253.x","article-title":"Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops","volume":"196","author":"RS Meyer","year":"2012","journal-title":"New Phytol"},{"issue":"5","key":"pgen.1012241.ref010","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1093\/aob\/mcy214","article-title":"Enset in Ethiopia: a poorly characterized but resilient starch staple","volume":"123","author":"JS Borrell","year":"2019","journal-title":"Ann Bot"},{"issue":"2","key":"pgen.1012241.ref011","doi-asserted-by":"crossref","first-page":"97","DOI":"10.2307\/4109206","article-title":"Classification of the bananas: the genus Ensete Horan","volume":"2","author":"EE Cheesman","year":"1947","journal-title":"Kew Bulletin"},{"issue":"3","key":"pgen.1012241.ref012","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1002\/ppp3.10084","article-title":"Enset\u2010based agricultural systems in Ethiopia: a systematic review of production trends, agronomy, processing and the wider food security applications of a neglected banana relative","volume":"2","author":"JS Borrell","year":"2020","journal-title":"Plants People Planet"},{"key":"pgen.1012241.ref013","volume-title":"Tree against hunger: enset-based agricultural systems in Ethiopia","author":"SA Brandt","year":"1997"},{"key":"pgen.1012241.ref014","first-page":"1","article-title":"Review of the history, taxonomy and nomenclature of ensete and the objectives and expectations of the international workshop on Ensete ventricosum (Welw.) Cheesman","volume":"17","author":"S Demissew","year":"2018","journal-title":"Ethiop J Biol Sci"},{"issue":"15","key":"pgen.1012241.ref015","doi-asserted-by":"crossref","first-page":"4165","DOI":"10.1111\/mec.17033","article-title":"Maintenance and expansion of genetic and trait variation following domestication in a clonal crop","volume":"32","author":"OW White","year":"2023","journal-title":"Mol Ecol"},{"issue":"3","key":"pgen.1012241.ref016","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1007\/s10722-023-01683-9","article-title":"Genetic diversity, population structure and selection signatures in Enset (Ensete ventricosum, (Welw.) Cheesman), an underutilized and key food security crop in Ethiopia","volume":"71","author":"AT Haile","year":"2023","journal-title":"Genet Resour Crop Evol"},{"issue":"1","key":"pgen.1012241.ref017","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1038\/s41438-020-00409-7","article-title":"Accumulation of mutations in genes associated with sexual reproduction contributed to the domestication of a vegetatively propagated staple crop, enset","volume":"7","author":"KG Tesfamicael","year":"2020","journal-title":"Hortic Res"},{"key":"pgen.1012241.ref018","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1007\/978-3-031-00848-1_19","article-title":"Genome resources for Ensete ventricosum (Enset) and related species","author":"L Venkatesan","year":"2022","journal-title":"Compendium of plant genomes"},{"key":"pgen.1012241.ref019","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/j.dib.2018.03.026","article-title":"Genome sequence data from 17 accessions of Ensete ventricosum, a staple food crop for millions in Ethiopia","volume":"18","author":"Z Yemataw","year":"2018","journal-title":"Data Brief"},{"issue":"2","key":"pgen.1012241.ref020","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1111\/j.1601-5223.2004.01792.x","article-title":"Distinction between wild and cultivated enset (Ensete ventricosum) gene pools in Ethiopia using RAPD markers","volume":"140","author":"G Birmeta","year":"2004","journal-title":"Hereditas"},{"key":"pgen.1012241.ref021","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1186\/s12863-015-0250-8","article-title":"Development of SSR markers and genetic diversity analysis in enset (Ensete ventricosum (Welw.) Cheesman), an orphan food security crop from Southern Ethiopia","volume":"16","author":"TM Olango","year":"2015","journal-title":"BMC Genet"},{"issue":"4","key":"pgen.1012241.ref022","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1111\/1755-0998.12351","article-title":"Estimating pairwise relatedness between individuals with different levels of ploidy","volume":"15","author":"K Huang","year":"2015","journal-title":"Mol Ecol Resour"},{"issue":"4","key":"pgen.1012241.ref023","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1111\/1755-0998.12217","article-title":"A pairwise relatedness estimator for polyploids","volume":"14","author":"K Huang","year":"2014","journal-title":"Mol Ecol Resour"},{"key":"pgen.1012241.ref024","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1111\/aab.12350","article-title":"Allometric equations for yield predictions of enset (Ensete ventricosum) and khat (Catha edulis) grown in home gardens of southern Ethiopia","volume":"171","author":"BT Mellisse","year":"2017","journal-title":"Ann Appl Biol"},{"issue":"1","key":"pgen.1012241.ref025","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/S0378-4290(00)00111-8","article-title":"Influence of repetitive transplanting and leaf pruning on dry matter and food production of enset (Ensete ventricosum Welw. (Cheesman))","volume":"68","author":"A Tsegaye","year":"2000","journal-title":"Field Crops Research"},{"issue":"6","key":"pgen.1012241.ref026","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1093\/aob\/mcaa122","article-title":"Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata)","volume":"126","author":"BM Sharif","year":"2020","journal-title":"Ann Bot"},{"key":"pgen.1012241.ref027","first-page":"1","article-title":"Population genomics of yams: evolution and domestication of Dioscorea species","author":"Y Sugihara","year":"2021"},{"issue":"6","key":"pgen.1012241.ref028","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0157712","article-title":"Genetic diversification and dispersal of taro (Colocasia esculenta (L.) Schott)","volume":"11","author":"H Cha\u00efr","year":"2016","journal-title":"PLoS One"},{"issue":"1","key":"pgen.1012241.ref029","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1002\/ppp3.10313","article-title":"Pedigree reconstruction for triploid apple cultivars using single nucleotide polymorphism array data","volume":"5","author":"NP Howard","year":"2022","journal-title":"Plants People Planet"},{"issue":"3","key":"pgen.1012241.ref030","doi-asserted-by":"crossref","first-page":"1266","DOI":"10.1111\/nph.15999","article-title":"Evolutionary associations between polyploidy, clonal reproduction, and perenniality in the angiosperms","volume":"224","author":"WE Van Drunen","year":"2019","journal-title":"New Phytol"},{"key":"pgen.1012241.ref031","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1086\/284115","article-title":"Polyploidy and novelty in flowering plants","volume":"122","author":"DA Levin","year":"1983","journal-title":"Am Nat"},{"issue":"11","key":"pgen.1012241.ref032","doi-asserted-by":"crossref","first-page":"2315","DOI":"10.1002\/ajb2.1759","article-title":"Short- and long-term consequences of genome doubling: a meta-analysis","volume":"108","author":"J Clo","year":"2021","journal-title":"Am J Bot"},{"key":"pgen.1012241.ref033","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1007\/s10457-012-9577-6","article-title":"Allometric equations for biomass estimation of Enset (Ensete ventricosum) grown in indigenous agroforestry systems in the Rift Valley escarpment of southern-eastern Ethiopia","volume":"87","author":"M Negash","year":"2013","journal-title":"Agrofor Syst"},{"key":"pgen.1012241.ref034","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1016\/j.plaphy.2021.03.041","article-title":"Improved response of triploid citrus varieties to water deficit is related to anatomical and cytological properties","volume":"162","author":"R Lourkisti","year":"2021","journal-title":"Plant Physiol Biochem"},{"issue":"18","key":"pgen.1012241.ref035","doi-asserted-by":"crossref","DOI":"10.1016\/j.cub.2022.07.019","article-title":"Polyploidy increases storage but decreases structural stability in Arabidopsis thaliana","volume":"32","author":"EK Pacey","year":"2022","journal-title":"Curr Biol"},{"issue":"4","key":"pgen.1012241.ref036","doi-asserted-by":"crossref","first-page":"5096","DOI":"10.1007\/s10668-020-00805-y","article-title":"Quantification of drought severity change in Ethiopia during 1952\u20132017","volume":"23","author":"AY Kassaye","year":"2020","journal-title":"Environ Dev Sustain"},{"issue":"1","key":"pgen.1012241.ref037","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1104\/pp.18.00967","article-title":"Polyploidy affects plant growth and alters cell wall composition","volume":"179","author":"S Corneillie","year":"2019","journal-title":"Plant Physiol"},{"issue":"4","key":"pgen.1012241.ref038","doi-asserted-by":"crossref","first-page":"1195","DOI":"10.1111\/nph.13881","article-title":"Genome size and ploidy influence angiosperm species\u2019 biomass under nitrogen and phosphorus limitation","volume":"210","author":"MS Guignard","year":"2016","journal-title":"New Phytol"},{"issue":"2","key":"pgen.1012241.ref039","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1111\/nph.13650","article-title":"Disaggregating polyploidy, parental genome dosage and hybridity contributions to heterosis in Arabidopsis thaliana","volume":"209","author":"A Fort","year":"2016","journal-title":"New Phytol"},{"issue":"7","key":"pgen.1012241.ref040","doi-asserted-by":"crossref","first-page":"2665","DOI":"10.1073\/pnas.1221966110","article-title":"Genomic dosage effects on heterosis in triploid maize","volume":"110","author":"H Yao","year":"2013","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"4","key":"pgen.1012241.ref041","doi-asserted-by":"crossref","first-page":"1808","DOI":"10.1104\/pp.112.208611","article-title":"Production of diploid male gametes in Arabidopsis by cold-induced destabilization of postmeiotic radial microtubule arrays","volume":"160","author":"N De Storme","year":"2012","journal-title":"Plant Physiol"},{"issue":"10","key":"pgen.1012241.ref042","doi-asserted-by":"crossref","first-page":"3587","DOI":"10.1093\/jxb\/err052","article-title":"Polyploidization mechanisms: temperature environment can induce diploid gamete formation in Rosa sp","volume":"62","author":"Y P\u00e9crix","year":"2011","journal-title":"J Exp Bot"},{"issue":"8","key":"pgen.1012241.ref043","doi-asserted-by":"crossref","first-page":"1895","DOI":"10.1046\/j.0962-1083.2001.01331.x","article-title":"Unmanaged sexual reproduction and the dynamics of genetic diversity of a vegetatively propagated crop plant, cassava (Manihot esculenta Crantz), in a traditional farming system","volume":"10","author":"M Elias","year":"2001","journal-title":"Mol Ecol"},{"issue":"9","key":"pgen.1012241.ref044","doi-asserted-by":"crossref","first-page":"2421","DOI":"10.1111\/j.1365-294X.2006.02958.x","article-title":"Farmers\u2019 use of wild relative and sexual reproduction in a vegetatively propagated crop. The case of yam in Benin","volume":"15","author":"N Scarcelli","year":"2006","journal-title":"Mol Ecol"},{"issue":"5","key":"pgen.1012241.ref045","doi-asserted-by":"crossref","first-page":"1879531","DOI":"10.1080\/15592324.2021.1879531","article-title":"Cultivation and possible domestication of feral and possibly wild yams (Dioscorea spp.) in Southwest Ethiopia: ethnobotanical and morphological evidence","volume":"16","author":"TB Worojie","year":"2021","journal-title":"Plant Signal Behav"},{"issue":"12","key":"pgen.1012241.ref046","doi-asserted-by":"crossref","first-page":"2146","DOI":"10.1094\/PHYTO-07-20-0311-RVW","article-title":"The vulnerability of bananas to globally emerging disease threats","volume":"111","author":"A Drenth","year":"2021","journal-title":"Phytopathology"},{"issue":"4","key":"pgen.1012241.ref047","doi-asserted-by":"crossref","first-page":"1979","DOI":"10.1534\/genetics.104.037788","article-title":"Aneuploidy and genetic variation in the Arabidopsis thaliana triploid response","volume":"170","author":"IM Henry","year":"2005","journal-title":"Genetics"},{"issue":"1","key":"pgen.1012241.ref048","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1146\/annurev.ecolsys.29.1.467","article-title":"Pathways, mechanisms, and rates of polyploid formation in flowering plants","volume":"29","author":"J Ramsey","year":"1998","journal-title":"Annu Rev Ecol Syst"},{"issue":"4","key":"pgen.1012241.ref049","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1508\/cytologia.69.387","article-title":"Relationships between meiotic irregularities and fertility in diploid and triploid Musa L","volume":"69","author":"MTV Adeleke","year":"2004","journal-title":"Cytologia"},{"key":"pgen.1012241.ref050","first-page":"11","article-title":"Male and female fertility in triploid grapes (Vitis complex) with special reference to the production of aneuploid plants","volume":"41","author":"SM Park","year":"2002","journal-title":"Vitis"},{"issue":"3","key":"pgen.1012241.ref051","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1111\/plb.13390","article-title":"Reproductive biology of wild and domesticated Ensete ventricosum: further evidence for maintenance of sexual reproductive capacity in a vegetatively propagated perennial crop","volume":"24","author":"S Tamrat","year":"2022","journal-title":"Plant Biol (Stuttg)"},{"issue":"2","key":"pgen.1012241.ref052","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1038\/s41592-020-01056-5","article-title":"Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm","volume":"18","author":"H Cheng","year":"2021","journal-title":"Nat Methods"},{"key":"pgen.1012241.ref053","doi-asserted-by":"crossref","first-page":"1287","DOI":"10.12688\/f1000research.12232.1","article-title":"BlobTools: interrogation of genome assemblies","volume":"6","author":"DR Laetsch","year":"2017","journal-title":"F1000Res"},{"issue":"9","key":"pgen.1012241.ref054","doi-asserted-by":"crossref","first-page":"2896","DOI":"10.1093\/bioinformatics\/btaa025","article-title":"Identifying and removing haplotypic duplication in primary genome assemblies","volume":"36","author":"D Guan","year":"2020","journal-title":"Bioinformatics"},{"issue":"3","key":"pgen.1012241.ref055","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1101\/gr.193474.115","article-title":"Chromosome-scale shotgun assembly using an in vitro method for long-range linkage","volume":"26","author":"NH Putnam","year":"2016","journal-title":"Genome Res"},{"issue":"14","key":"pgen.1012241.ref056","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"4","key":"pgen.1012241.ref057","article-title":"NOVOPlasty: de novo assembly of organelle genomes from whole genome data","volume":"45","author":"N Dierckxsens","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"pgen.1012241.ref058","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"C Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"issue":"6","key":"pgen.1012241.ref059","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"AR Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"pgen.1012241.ref060","doi-asserted-by":"crossref","first-page":"713216","DOI":"10.3389\/fpls.2021.713216","article-title":"Reassessing banana phylogeny and organelle inheritance modes using genome skimming data","volume":"12","author":"C-S Wu","year":"2021","journal-title":"Front Plant Sci"},{"issue":"17","key":"pgen.1012241.ref061","doi-asserted-by":"crossref","first-page":"9451","DOI":"10.1073\/pnas.1921046117","article-title":"RepeatModeler2 for automated genomic discovery of transposable element families","volume":"117","author":"JM Flynn","year":"2020","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pgen.1012241.ref062","unstructured":"Smit AFA, Hubley R, Green P. RepeatMasker Open-4.0. 2013\u20132015. 2015."},{"key":"pgen.1012241.ref063","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giac027","article-title":"A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae","volume":"11","author":"Z Wang","year":"2022","journal-title":"Gigascience"},{"issue":"7410","key":"pgen.1012241.ref064","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/nature11241","article-title":"The banana (Musa acuminata) genome and the evolution of monocotyledonous plants","volume":"488","author":"A D\u2019Hont","year":"2012","journal-title":"Nature"},{"key":"pgen.1012241.ref065","article-title":"RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms","volume":"6","author":"Z Hao","year":"2020","journal-title":"PeerJ Comput Sci"},{"issue":"15","key":"pgen.1012241.ref066","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":"1","key":"pgen.1012241.ref067","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.1012241.ref068","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"},{"key":"pgen.1012241.ref069","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gky1053","article-title":"OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs","volume":"47","author":"EV Kriventseva","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"pgen.1012241.ref070","doi-asserted-by":"crossref","DOI":"10.1093\/hr\/uhac221","article-title":"The banana genome hub: a community database for genomics in the Musaceae","volume":"9","author":"G Droc","year":"2022","journal-title":"Hortic Res"},{"issue":"1","key":"pgen.1012241.ref071","article-title":"BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database","volume":"3","author":"T Br\u016fna","year":"2021","journal-title":"NAR Genom Bioinform"},{"issue":"5","key":"pgen.1012241.ref072","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1093\/bioinformatics\/btv661","article-title":"BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS","volume":"32","author":"KJ Hoff","year":"2016","journal-title":"Bioinformatics"},{"issue":"4","key":"pgen.1012241.ref073","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1093\/bioinformatics\/btw663","article-title":"KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies","volume":"33","author":"D Mapleson","year":"2017","journal-title":"Bioinformatics"},{"issue":"1","key":"pgen.1012241.ref074","doi-asserted-by":"crossref","first-page":"1432","DOI":"10.1038\/s41467-020-14998-3","article-title":"GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes","volume":"11","author":"TR Ranallo-Benavidez","year":"2020","journal-title":"Nat Commun"},{"issue":"10","key":"pgen.1012241.ref075","doi-asserted-by":"crossref","first-page":"4647","DOI":"10.1093\/molbev\/msab199","article-title":"BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes","volume":"38","author":"M Manni","year":"2021","journal-title":"Mol Biol Evol"},{"key":"pgen.1012241.ref076","doi-asserted-by":"crossref","first-page":"170122","DOI":"10.1038\/sdata.2017.122","article-title":"Climatologies at high resolution for the earth\u2019s land surface areas","volume":"4","author":"DN Karger","year":"2017","journal-title":"Sci Data"},{"key":"pgen.1012241.ref077","author":"D Karger","year":"2017"},{"issue":"1","key":"pgen.1012241.ref078","doi-asserted-by":"crossref","first-page":"21455","DOI":"10.1038\/s41598-020-78589-4","article-title":"GRAS-Di system facilitates high-density genetic map construction and QTL identification in recombinant inbred lines of the wheat progenitor Aegilops tauschii","volume":"10","author":"Y Miki","year":"2020","journal-title":"Sci Rep"},{"key":"pgen.1012241.ref079","author":"E Garrison","year":"2012"},{"issue":"15","key":"pgen.1012241.ref080","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":"1","key":"pgen.1012241.ref081","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1111\/1755-0998.12549","article-title":"vcfr: a package to manipulate and visualize variant call format data in R","volume":"17","author":"BJ Knaus","year":"2017","journal-title":"Mol Ecol Resour"},{"key":"pgen.1012241.ref082","author":"P Poncet","year":"2019"},{"issue":"6","key":"pgen.1012241.ref083","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1093\/bioinformatics\/btr011","article-title":"A fast, lock-free approach for efficient parallel counting of occurrences of k-mers","volume":"27","author":"G Mar\u00e7ais","year":"2011","journal-title":"Bioinformatics"},{"issue":"2","key":"pgen.1012241.ref084","doi-asserted-by":"crossref","first-page":"624","DOI":"10.1016\/j.ympev.2011.11.003","article-title":"Speciation and evolution in the Gagea reticulata species complex (Tulipeae; Liliaceae)","volume":"62","author":"M Zarrei","year":"2012","journal-title":"Mol Phylogenet Evol"},{"issue":"3","key":"pgen.1012241.ref085","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1093\/jhered\/esy006","article-title":"The analysis of polyploid genetic data","volume":"109","author":"PG Meirmans","year":"2018","journal-title":"J Hered"},{"key":"pgen.1012241.ref086","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.281","article-title":"Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and\/or sexual reproduction","volume":"2","author":"ZN Kamvar","year":"2014","journal-title":"PeerJ"},{"issue":"24","key":"pgen.1012241.ref087","doi-asserted-by":"crossref","first-page":"5115","DOI":"10.1111\/j.1365-294X.2007.03535.x","article-title":"Standardizing methods to address clonality in population studies","volume":"16","author":"S Arnaud-Haond","year":"2007","journal-title":"Mol Ecol"},{"key":"pgen.1012241.ref088","author":"J Oksanen","year":"2022"},{"key":"pgen.1012241.ref089","first-page":"1","article-title":"FactoMineR: an R package for multivariate analysis","volume":"25","author":"S L\u00ea","year":"2008","journal-title":"J Stat Softw"},{"issue":"5","key":"pgen.1012241.ref090","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1111\/1755-0998.12129","article-title":"StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations","volume":"13","author":"LW Pembleton","year":"2013","journal-title":"Mol Ecol Resour"},{"issue":"3","key":"pgen.1012241.ref091","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1534\/genetics.118.301468","article-title":"Genotyping polyploids from messy sequencing data","volume":"210","author":"D Gerard","year":"2018","journal-title":"Genetics"},{"issue":"6","key":"pgen.1012241.ref092","doi-asserted-by":"crossref","first-page":"1795","DOI":"10.1093\/bioinformatics\/btz852","article-title":"Priors for genotyping polyploids","volume":"36","author":"D Gerard","year":"2020","journal-title":"Bioinformatics"},{"issue":"5","key":"pgen.1012241.ref093","doi-asserted-by":"crossref","first-page":"1434","DOI":"10.1111\/1755-0998.13330","article-title":"Model-based genotype and ancestry estimation for potential hybrids with mixed-ploidy","volume":"21","author":"V Shastry","year":"2021","journal-title":"Mol Ecol Resour"},{"key":"pgen.1012241.ref094","first-page":"3571","article-title":"Asymptotic aquivalence of Bayes cross validation and widely applicable information criterion in singular learning theory","volume":"11","author":"S Watanabe","year":"2010","journal-title":"J Mach Learn Res"},{"key":"pgen.1012241.ref095","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v080.i01","article-title":"brms: an R package for Bayesian multilevel models using Stan","volume":"80","author":"PC B\u00fcrkner","year":"2017","journal-title":"J Stat Softw"},{"key":"pgen.1012241.ref096","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v076.i01","article-title":"Stan: A probabilistic programming language","volume":"76","author":"B Carpenter","year":"2017","journal-title":"J Stat Softw"}],"updated-by":[{"DOI":"10.1371\/journal.pgen.1012241","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,7,31]],"date-time":"2026-07-31T00:00:00Z","timestamp":1785456000000}}],"container-title":["PLOS Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1012241","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,31]],"date-time":"2026-07-31T17:42:03Z","timestamp":1785519723000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1012241"}},"subtitle":[],"editor":[{"given":"Jae Young","family":"Choi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,7,24]]},"references-count":96,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2026,7,24]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1012241","relation":{},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,24]]}}}