{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T18:25:18Z","timestamp":1787250318745,"version":"build-2736575974"},"update-to":[{"DOI":"10.1371\/journal.pgen.1011820","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T00:00:00Z","timestamp":1787184000000}}],"reference-count":107,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T00:00:00Z","timestamp":1786579200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100010761","name":"Syngenta International","doi-asserted-by":"publisher","award":["15000441"],"award-info":[{"award-number":["15000441"]}],"id":[{"id":"10.13039\/501100010761","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100018956","name":"Laboratoire d'Excellence TULIP","doi-asserted-by":"publisher","award":["ANR-10-LABX-41"],"award-info":[{"award-number":["ANR-10-LABX-41"]}],"id":[{"id":"10.13039\/100018956","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010761","name":"Syngenta International","doi-asserted-by":"publisher","award":["No. Z09604"],"award-info":[{"award-number":["No. Z09604"]}],"id":[{"id":"10.13039\/501100010761","id-type":"DOI","asserted-by":"publisher"}]},{"name":"SYNGENTA-ANRT","award":["ANRT 2021\/1695"],"award-info":[{"award-number":["ANRT 2021\/1695"]}]}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"abstract":"<jats:p>\n                    Ongoing climate change is driving unprecedented environmental fluctuations, with extreme events predicted to increase in frequency, intensity and duration. Among climatic parameters, temperature is expected to fluctuate the most by the end of the century and its elevation has already demonstrated to pose a major challenge to plant health. In this context, understanding how temperature modulates plant-pathogen interactions and their underlying genetic architecture is critical. Bacterial wilt, caused by strains of the\n                    <jats:italic>Ralstonia solanacearum<\/jats:italic>\n                    species complex, is a devastating disease affecting many plant species. Genetic resistance remains the most effective control strategy. In tomato, resistance is quantitative and mostly relies on quantitative trait loci (QTLs)\n                    <jats:italic>bwr-6<\/jats:italic>\n                    and\n                    <jats:italic>bwr-12<\/jats:italic>\n                    . However, as in other crops, high temperature and humidity can compromise this resistance in commercial tomato cultivars. We investigated temperature-dependent quantitative disease resistance (QDR) using a panel of 189 wild tomato accessions, predominantly\n                    <jats:italic>Solanum pimpinellifolium<\/jats:italic>\n                    , representing genetic diversity from contrasting ecological conditions. Disease progression was monitored from three to ten days post-inoculation at 28 \u00b0C and 32 \u00b0C, using a time-course phenotyping approach. Genome-wide association (GWA) analyses were performed, based on daily symptom scores and two reference genomes, to account for structural variations and improve QTL detection. This strategy identified 44 candidate genes and revealed a temporally dynamic genetic architecture of the plant response. Strikingly, no candidate genes were shared between temperatures, supporting distinct genetic determinants under different temperature conditions. Many candidate genes were expressed in roots and belong to gene families involved in plant immunity, with two candidates co-localizing with\n                    <jats:italic>bwr-6<\/jats:italic>\n                    and\n                    <jats:italic>bwr-12<\/jats:italic>\n                    , whose causal genes remain unknown. Altogether, our findings demonstrate that resistance to bacterial wilt in wild tomato is flexible, environment-dependent, and temporally dynamic, highlighting the importance of integrating environmental context and genomic diversity to better understand plant-pathogen interactions.\n                  <\/jats:p>","DOI":"10.1371\/journal.pgen.1011820","type":"journal-article","created":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T17:42:22Z","timestamp":1786642942000},"page":"e1011820","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["New biologically relevant resistance to bacterial wilt in heat-stressed tomato revealed by two-reference Genome Wide Association"],"prefix":"10.1371","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-9853-752X","authenticated-orcid":true,"given":"Adrien","family":"Belny","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henri","family":"Desaint","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Myl\u00e8ne","family":"Rigal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2348-0778","authenticated-orcid":true,"given":"S\u00e9bastien","family":"Carr\u00e8re","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00e9r\u00f4me","family":"Gouzy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-7808-2776","authenticated-orcid":true,"given":"Gregori","family":"Bonnet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-9812-8998","authenticated-orcid":true,"given":"C\u00e9line","family":"Labourey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5060-4505","authenticated-orcid":true,"given":"Elise","family":"Albert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurent","family":"Grivet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8059-5638","authenticated-orcid":true,"given":"Fabrice","family":"Roux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabienne","family":"Vailleau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3839-9067","authenticated-orcid":true,"given":"Tristan","family":"Mary-Huard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4781-6210","authenticated-orcid":true,"given":"Richard","family":"Berthom\u00e9","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,8,13]]},"reference":[{"issue":"4","key":"pgen.1011820.ref001","doi-asserted-by":"crossref","first-page":"1020","DOI":"10.1093\/jxb\/eraa531","article-title":"Every cloud has a silver lining: how abiotic stresses affect gene expression in plant-pathogen interactions","volume":"72","author":"M Zarattini","year":"2021","journal-title":"J Exp Bot"},{"key":"pgen.1011820.ref002","doi-asserted-by":"crossref","first-page":"153764","DOI":"10.1016\/j.jplph.2022.153764","article-title":"Climate change-associated multifactorial stress combination: A present challenge for our ecosystems","volume":"276","author":"LS Pascual","year":"2022","journal-title":"J Plant Physiol"},{"issue":"2","key":"pgen.1011820.ref003","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1111\/nph.16965","article-title":"Fight hard or die trying: when plants face pathogens under heat stress","volume":"229","author":"H Desaint","year":"2021","journal-title":"New Phytol"},{"key":"pgen.1011820.ref004","first-page":"184","article-title":"Climate Change 2023: Synthesis Report.","volume-title":"Contribution of Working Groups I, II and III to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change","author":"IPCC","year":"2023"},{"issue":"5","key":"pgen.1011820.ref005","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1038\/ismej.2011.160","article-title":"Contrasting recombination patterns and demographic histories of the plant pathogen Ralstonia solanacearum inferred from MLSA","volume":"6","author":"E Wicker","year":"2012","journal-title":"ISME J"},{"key":"pgen.1011820.ref006","first-page":"9","article-title":"The current bacterial wilt situation: a global overview.","volume-title":"Bacterial wilt disease and the Ralstonia solanacearum complex","author":"JG. 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(Burholderia) solanacearum in the stem tissues","volume":"45","author":"P Prior","year":"1996","journal-title":"Plant Pathology"},{"issue":"7","key":"pgen.1011820.ref043","doi-asserted-by":"crossref","first-page":"909","DOI":"10.1094\/Phyto-67-909","article-title":"Effect of soil temperature on resistance of tomato cultivars to bacterial wilt","volume":"77","author":"TW Mew","year":"1977","journal-title":"Phytopathology"},{"issue":"10","key":"pgen.1011820.ref044","doi-asserted-by":"crossref","first-page":"3542","DOI":"10.1128\/AEM.04123-14","article-title":"Tropical strains of Ralstonia solanacearum outcompete race 3 biovar 2 strains at lowland tropical temperatures","volume":"81","author":"AI Huerta","year":"2015","journal-title":"Appl Environ Microbiol"},{"issue":"5","key":"pgen.1011820.ref045","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1093\/aob\/mcm150","article-title":"Domestication and breeding of tomatoes: what have we gained and what can we gain in the future?","volume":"100","author":"Y Bai","year":"2007","journal-title":"Ann Bot"},{"issue":"1","key":"pgen.1011820.ref046","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s12864-015-1444-1","article-title":"Genomic variation in tomato, from wild ancestors to contemporary breeding accessions","volume":"16","author":"J Blanca","year":"2015","journal-title":"BMC Genomics"},{"key":"pgen.1011820.ref047","author":"P Massicotte","year":"2026"},{"issue":"3","key":"pgen.1011820.ref048","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1080\/17538947.2020.1829112","article-title":"ClimateCharts.net - an interactive climate analysis web platform","volume":"14","author":"L Zepner","year":"2021","journal-title":"Int J Digit Earth"},{"key":"pgen.1011820.ref049","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.78526","article-title":"GENESPACE tracks regions of interest and gene copy number variation across multiple genomes","volume":"11","author":"JT Lovell","year":"2022","journal-title":"Elife"},{"key":"pgen.1011820.ref050","first-page":"1","article-title":"An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps","author":"PS Hosmani","year":"2019","journal-title":"bioRxiv"},{"issue":"1","key":"pgen.1011820.ref051","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/j.cell.2020.05.021","article-title":"Major impacts of widespread structural variation on gene expression and crop improvement in tomato","volume":"182","author":"A Michael","year":"2020","journal-title":"Cell"},{"key":"pgen.1011820.ref052","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1007\/978-1-4939-7604-1_18","article-title":"Plant pathogenicity phenotyping of Ralstonia solanacearum strains","volume":"1734","author":"A Morel","year":"2018","journal-title":"Methods Mol 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Zhou","year":"2022","journal-title":"Nature"},{"key":"pgen.1011820.ref062","doi-asserted-by":"crossref","first-page":"1402","DOI":"10.3389\/fpls.2018.01402","article-title":"The genome sequence of the wild tomato Solanum pimpinellifolium provides insights into salinity tolerance","volume":"9","author":"R Razali","year":"2018","journal-title":"Front Plant Sci"},{"issue":"2","key":"pgen.1011820.ref063","article-title":"Multiple maize reference genomes impact the identification of variants by genome-wide association study in a diverse inbred panel","volume":"12","author":"JL Gage","year":"2019","journal-title":"Plant Genome"},{"issue":"11","key":"pgen.1011820.ref064","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1011801","article-title":"Combined reference-free and multi-reference based GWAS uncover cryptic variation underlying rapid adaptation in a fungal plant pathogen","volume":"19","author":"A Dutta","year":"2023","journal-title":"PLoS Pathog"},{"issue":"7117","key":"pgen.1011820.ref065","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1038\/nature05286","article-title":"The plant immune system","volume":"444","author":"JDG Jones","year":"2006","journal-title":"Nature"},{"issue":"2","key":"pgen.1011820.ref066","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1111\/tpj.15462","article-title":"Network organization of the plant immune system: from pathogen perception to robust defense induction","volume":"109","author":"F Delplace","year":"2022","journal-title":"Plant J"},{"issue":"1","key":"pgen.1011820.ref067","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1104\/pp.108.121038","article-title":"Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection","volume":"148","author":"JT Ascencio-Ib\u00e1\u00f1ez","year":"2008","journal-title":"Plant Physiol"},{"issue":"4","key":"pgen.1011820.ref068","doi-asserted-by":"crossref","first-page":"1890","DOI":"10.1104\/pp.105.067223","article-title":"Pathogen-responsive expression of glycosyltransferase genes UGT73B3 and UGT73B5 is necessary for resistance to Pseudomonas syringae pv tomato in Arabidopsis","volume":"139","author":"M Langlois-Meurinne","year":"2005","journal-title":"Plant Physiol"},{"issue":"3","key":"pgen.1011820.ref069","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1007\/s10142-006-0041-4","article-title":"Suppression by ABA of salicylic acid and lignin accumulation and the expression of multiple genes, in Arabidopsis infected with Pseudomonas syringae pv. tomato","volume":"7","author":"PG Mohr","year":"2007","journal-title":"Funct Integr Genomics"},{"issue":"2","key":"pgen.1011820.ref070","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1093\/plphys\/kiac103","article-title":"Tomato brown rugose fruit virus resistance generated by quadruple knockout of homologs of TOBAMOVIRUS MULTIPLICATION1 in tomato","volume":"189","author":"M Ishikawa","year":"2022","journal-title":"Plant Physiol"},{"issue":"2","key":"pgen.1011820.ref071","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1093\/emboj\/cdg034","article-title":"Arabidopsis tobamovirus multiplication (TOM) 2 locus encodes a transmembrane protein that interacts with TOM1","volume":"22","author":"Y Tsujimoto","year":"2003","journal-title":"The EMBO Journal"},{"issue":"11","key":"pgen.1011820.ref072","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1094\/MPMI-03-23-0032-R","article-title":"The Sw-5b NLR immune receptor induces early transcriptional changes in response to thrips and mechanical modes of inoculation of tomato spotted wilt orthotospovirus","volume":"36","author":"NA Ordaz","year":"2023","journal-title":"Mol Plant-Microbe Interact"},{"key":"pgen.1011820.ref073","doi-asserted-by":"crossref","first-page":"1004406","DOI":"10.3389\/fpls.2022.1004406","article-title":"Is there a specific calcium signal out there to decode combined biotic stress and temperature elevation?","volume":"13","author":"S Carpentier","year":"2022","journal-title":"Front Plant Sci"},{"issue":"5","key":"pgen.1011820.ref074","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1007\/s00122-018-3054-1","article-title":"Identification of a molecular marker tightly linked to bacterial wilt resistance in tomato by genome-wide SNP analysis","volume":"131","author":"B Kim","year":"2018","journal-title":"Theor Appl Genet"},{"issue":"3","key":"pgen.1011820.ref075","doi-asserted-by":"crossref","first-page":"1314","DOI":"10.1104\/pp.19.01060","article-title":"The calmodulin-binding protein IQM1 interacts with CATALASE2 to affect pathogen defense","volume":"181","author":"T Lv","year":"2019","journal-title":"Plant Physiol"},{"issue":"11","key":"pgen.1011820.ref076","article-title":"Emerging roles of receptor-like proteins in plant immunity: crosstalk, signalling networks and prospects for disease resistance breeding","volume":"26","author":"C Gao","year":"2025","journal-title":"Mol Plant Pathol"},{"issue":"5","key":"pgen.1011820.ref077","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1007\/s00122-018-3054-1","article-title":"Identification of a molecular marker tightly linked to bacterial wilt resistance in tomato by genome-wide SNP analysis","volume":"131","author":"B Kim","year":"2018","journal-title":"Theor Appl Genet"},{"issue":"6861","key":"pgen.1011820.ref078","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1038\/35104586","article-title":"Mechanism of ubiquitin activation revealed by the structure of a bacterial MoeB-MoaD complex","volume":"414","author":"MW Lake","year":"2001","journal-title":"Nature"},{"key":"pgen.1011820.ref079","doi-asserted-by":"crossref","first-page":"739","DOI":"10.3389\/fpls.2014.00739","article-title":"Subtilisin-like proteases in plant-pathogen recognition and immune priming: a perspective","volume":"5","author":"A Figueiredo","year":"2014","journal-title":"Front Plant Sci"},{"issue":"6493","key":"pgen.1011820.ref080","doi-asserted-by":"crossref","DOI":"10.1126\/science.aba5435","article-title":"Horizontal gene transfer of Fhb7 from fungus underlies Fusarium head blight resistance in wheat","volume":"368","author":"H Wang","year":"2020","journal-title":"Science"},{"issue":"1","key":"pgen.1011820.ref081","doi-asserted-by":"crossref","first-page":"1534","DOI":"10.1038\/s41467-019-09462-w","article-title":"Meta-analysis of genome-wide association studies provides insights into genetic control of tomato flavor","volume":"10","author":"J Zhao","year":"2019","journal-title":"Nat Commun"},{"issue":"2","key":"pgen.1011820.ref082","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1007\/s10681-012-0830-x","article-title":"Identification of major QTLs associated with stable resistance of tomato cultivar \u2018Hawaii 7996\u2019 to Ralstonia solanacearum","volume":"190","author":"J-F Wang","year":"2012","journal-title":"Euphytica"},{"issue":"1","key":"pgen.1011820.ref083","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1111\/tpj.12616","article-title":"Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing","volume":"80","author":"100 Tomato Genome Sequencing Consortium","year":"2014","journal-title":"Plant J"},{"issue":"10","key":"pgen.1011820.ref084","doi-asserted-by":"crossref","first-page":"924","DOI":"10.1094\/PHYTO-12-11-0342","article-title":"Diversity among Ralstonia solanacearum strains isolated from the southeastern United States","volume":"102","author":"JC Hong","year":"2012","journal-title":"Phytopathology"},{"issue":"6871","key":"pgen.1011820.ref085","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1038\/415497a","article-title":"Genome sequence of the plant pathogen Ralstonia solanacearum","volume":"415","author":"M Salanoubat","year":"2002","journal-title":"Nature"},{"issue":"4","key":"pgen.1011820.ref086","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1128\/JB.01189-09","article-title":"PrhG, a transcriptional regulator responding to growth conditions, is involved in the control of the type III secretion system regulon in Ralstonia solanacearum","volume":"192","author":"L Plener","year":"2010","journal-title":"J Bacteriol"},{"issue":"6","key":"pgen.1011820.ref087","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1038\/s41588-018-0110-3","article-title":"The Rosa genome provides new insights into the domestication of modern roses","volume":"50","author":"O Raymond","year":"2018","journal-title":"Nat Genet"},{"issue":"5","key":"pgen.1011820.ref088","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1101\/gr.215087.116","article-title":"Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation","volume":"27","author":"S Koren","year":"2017","journal-title":"Genome Res"},{"key":"pgen.1011820.ref089","first-page":"97","article-title":"EuGene: An Automated Integrative Gene Finder for Eukaryotes and Prokaryotes.","volume-title":"Gene Prediction. 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Sciences Agronomiques","author":"A Gallais","year":"1989"},{"key":"pgen.1011820.ref103","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v082.i13","article-title":"lmerTest package: Tests in linear mixed effects models","volume":"82","author":"A Kuznetsova","year":"2017","journal-title":"J Stat Softw"},{"issue":"3","key":"pgen.1011820.ref104","doi-asserted-by":"crossref","first-page":"250","DOI":"10.3835\/plantgenome2011.08.0024","article-title":"Ridge regression and other kernels for genomic selection with R package rrBLUP","volume":"4","author":"JB Endelman","year":"2011","journal-title":"The Plant Genome"},{"issue":"4","key":"pgen.1011820.ref105","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1038\/s41437-019-0235-x","article-title":"A local score approach improves GWAS resolution and detects minor QTL: application to Medicago truncatula quantitative disease resistance to multiple Aphanomyces euteiches isolates","volume":"123","author":"M Bonhomme","year":"2019","journal-title":"Heredity (Edinb)"},{"issue":"22","key":"pgen.1011820.ref106","doi-asserted-by":"crossref","first-page":"10881","DOI":"10.1093\/nar\/16.22.10881","article-title":"Multiple sequence alignment with hierarchical clustering","volume":"16","author":"F Corpet","year":"1988","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pgen.1011820.ref107","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"}],"updated-by":[{"DOI":"10.1371\/journal.pgen.1011820","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T00:00:00Z","timestamp":1787184000000}}],"container-title":["PLOS Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1011820","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T17:46:14Z","timestamp":1787247974000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1011820"}},"subtitle":[],"editor":[{"given":"Tatiana","family":"Giraud","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,8,13]]},"references-count":107,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2026,8,13]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1011820","relation":{},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,13]]}}}