{"id":"https://openalex.org/W7212029957","doi":"https://doi.org/10.64898/2026.09.04.749403","title":"Large parallel deletions are associated with massive gene losses and virulence acquisition in Meloidogyne incognita","display_name":"Large parallel deletions are associated with massive gene losses and virulence acquisition in Meloidogyne incognita","publication_year":2026,"publication_date":"2026-09-08","ids":{"openalex":"https://openalex.org/W7212029957","doi":"https://doi.org/10.64898/2026.09.04.749403"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.04.749403","doi":"https://doi.org/10.64898/2026.09.04.749403","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.04.749403","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/08/2026.09.04.749403.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/08/2026.09.04.749403.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014719864","display_name":"Ana Paula Zotta Mota","orcid":"https://orcid.org/0000-0003-3251-1406","observed_orcids":["https://orcid.org/0000-0003-3251-1406"]},"institutions":[{"id":"https://openalex.org/I201841394","display_name":"Universit\u00e9 C\u00f4te d'Azur","ror":"https://ror.org/019tgvf94","country_code":"FR","type":"education","lineage":["https://openalex.org/I201841394"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210153141","display_name":"Institut Sophia Agrobiotech","ror":"https://ror.org/04vj6zn89","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I201841394","https://openalex.org/I4210088668","https://openalex.org/I4210096427","https://openalex.org/I4210153141"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Ana Paula Zotta Mota","raw_affiliation_strings":["INRAE, Universit\u00e9 C\u00f4te d\u2019Azur, Institut Sophia Agrobiotech, Sophia Antipolis, France"],"raw_orcid":"https://orcid.org/0000-0003-3251-1406","affiliations":[{"raw_affiliation_string":"INRAE, Universit\u00e9 C\u00f4te d\u2019Azur, Institut Sophia Agrobiotech, Sophia Antipolis, France","institution_ids":["https://openalex.org/I201841394","https://openalex.org/I4210088668","https://openalex.org/I4210153141"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100558036","display_name":"Yu Hongli","orcid":"https://orcid.org/0009-0005-5715-9260","observed_orcids":["https://orcid.org/0009-0005-5715-9260"]},"institutions":[{"id":"https://openalex.org/I201841394","display_name":"Universit\u00e9 C\u00f4te d'Azur","ror":"https://ror.org/019tgvf94","country_code":"FR","type":"education","lineage":["https://openalex.org/I201841394"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210153141","display_name":"Institut Sophia Agrobiotech","ror":"https://ror.org/04vj6zn89","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I201841394","https://openalex.org/I4210088668","https://openalex.org/I4210096427","https://openalex.org/I4210153141"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Hongli Yu","raw_affiliation_strings":["INRAE, Universit\u00e9 C\u00f4te d\u2019Azur, Institut Sophia Agrobiotech, Sophia Antipolis, France"],"raw_orcid":"https://orcid.org/0009-0005-5715-9260","affiliations":[{"raw_affiliation_string":"INRAE, Universit\u00e9 C\u00f4te d\u2019Azur, Institut Sophia Agrobiotech, Sophia Antipolis, France","institution_ids":["https://openalex.org/I201841394","https://openalex.org/I4210088668","https://openalex.org/I4210153141"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5116581103","display_name":"maxime multari","orcid":"https://orcid.org/0009-0001-4704-3580","observed_orcids":["https://orcid.org/0009-0001-4704-3580"]},"institutions":[{"id":"https://openalex.org/I201841394","display_name":"Universit\u00e9 C\u00f4te d'Azur","ror":"https://ror.org/019tgvf94","country_code":"FR","type":"education","lineage":["https://openalex.org/I201841394"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210153141","display_name":"Institut Sophia Agrobiotech","ror":"https://ror.org/04vj6zn89","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I201841394","https://openalex.org/I4210088668","https://openalex.org/I4210096427","https://openalex.org/I4210153141"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Maxime Multari","raw_affiliation_strings":["INRAE, Universit\u00e9 C\u00f4te d\u2019Azur, Institut Sophia Agrobiotech, Sophia Antipolis, France"],"raw_orcid":"https://orcid.org/0009-0001-4704-3580","affiliations":[{"raw_affiliation_string":"INRAE, Universit\u00e9 C\u00f4te d\u2019Azur, Institut Sophia Agrobiotech, Sophia Antipolis, France","institution_ids":["https://openalex.org/I201841394","https://openalex.org/I4210088668","https://openalex.org/I4210153141"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041756399","display_name":"Rahim Hassanaly-Goulamhoussen","orcid":"https://orcid.org/0000-0002-0811-7217","observed_orcids":["https://orcid.org/0000-0002-0811-7217"]},"institutions":[{"id":"https://openalex.org/I201841394","display_name":"Universit\u00e9 C\u00f4te d'Azur","ror":"https://ror.org/019tgvf94","country_code":"FR","type":"education","lineage":["https://openalex.org/I201841394"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210153141","display_name":"Institut Sophia Agrobiotech","ror":"https://ror.org/04vj6zn89","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I201841394","https://openalex.org/I4210088668","https://openalex.org/I4210096427","https://openalex.org/I4210153141"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Rahim Hassanaly Goulamhoussen","raw_affiliation_strings":["INRAE, Universit\u00e9 C\u00f4te d\u2019Azur, Institut Sophia Agrobiotech, Sophia Antipolis, France"],"raw_orcid":"https://orcid.org/0000-0002-0811-7217","affiliations":[{"raw_affiliation_string":"INRAE, Universit\u00e9 C\u00f4te d\u2019Azur, Institut Sophia Agrobiotech, Sophia Antipolis, France","institution_ids":["https://openalex.org/I201841394","https://openalex.org/I4210088668","https://openalex.org/I4210153141"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113694946","display_name":"Laetitia Perfus\u2010Barbeoch","orcid":"https://orcid.org/0000-0003-4395-7913","observed_orcids":["https://orcid.org/0000-0003-4395-7913"]},"institutions":[{"id":"https://openalex.org/I201841394","display_name":"Universit\u00e9 C\u00f4te d'Azur","ror":"https://ror.org/019tgvf94","country_code":"FR","type":"education","lineage":["https://openalex.org/I201841394"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210153141","display_name":"Institut Sophia Agrobiotech","ror":"https://ror.org/04vj6zn89","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I201841394","https://openalex.org/I4210088668","https://openalex.org/I4210096427","https://openalex.org/I4210153141"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Laetitia Perfus-Barbeoch","raw_affiliation_strings":["INRAE, Universit\u00e9 C\u00f4te d\u2019Azur, Institut Sophia Agrobiotech, Sophia Antipolis, France"],"raw_orcid":"https://orcid.org/0000-0003-4395-7913","affiliations":[{"raw_affiliation_string":"INRAE, Universit\u00e9 C\u00f4te d\u2019Azur, Institut Sophia Agrobiotech, Sophia Antipolis, France","institution_ids":["https://openalex.org/I201841394","https://openalex.org/I4210088668","https://openalex.org/I4210153141"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062337599","display_name":"Sophie Vali\u00e8re","orcid":"https://orcid.org/0009-0000-3430-7164","observed_orcids":["https://orcid.org/0009-0000-3430-7164"]},"institutions":[{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4405263539","display_name":"Genotoul coordination","ror":"https://ror.org/02f0kwz92","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I4210088668","https://openalex.org/I4405263539"]},{"id":"https://openalex.org/I4405263673","display_name":"G\u00e9nome et Transcriptome - Plateforme G\u00e9nomique","ror":"https://ror.org/04kph4f16","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4405263673"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Sophie Vali\u00e8re","raw_affiliation_strings":["INRAE, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France"],"raw_orcid":"https://orcid.org/0009-0000-3430-7164","affiliations":[{"raw_affiliation_string":"INRAE, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France","institution_ids":["https://openalex.org/I4210088668","https://openalex.org/I4405263539","https://openalex.org/I4405263673"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128875677","display_name":"Kory Jason","orcid":"https://orcid.org/0009-0001-0487-1650","observed_orcids":["https://orcid.org/0009-0001-0487-1650"]},"institutions":[{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4405263539","display_name":"Genotoul coordination","ror":"https://ror.org/02f0kwz92","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I4210088668","https://openalex.org/I4405263539"]},{"id":"https://openalex.org/I4405263673","display_name":"G\u00e9nome et Transcriptome - Plateforme G\u00e9nomique","ror":"https://ror.org/04kph4f16","country_code":"FR","type":"facility","lineage":["https://openalex.org/I4210088668","https://openalex.org/I4405263673"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Kory Jason","raw_affiliation_strings":["INRAE, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France"],"raw_orcid":"https://orcid.org/0009-0001-0487-1650","affiliations":[{"raw_affiliation_string":"INRAE, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France","institution_ids":["https://openalex.org/I4210088668","https://openalex.org/I4405263539","https://openalex.org/I4405263673"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066120393","display_name":"Philippe Castagnone\u2010Sereno","orcid":"https://orcid.org/0000-0003-2048-9651","observed_orcids":["https://orcid.org/0000-0003-2048-9651"]},"institutions":[{"id":"https://openalex.org/I201841394","display_name":"Universit\u00e9 C\u00f4te d'Azur","ror":"https://ror.org/019tgvf94","country_code":"FR","type":"education","lineage":["https://openalex.org/I201841394"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210153141","display_name":"Institut Sophia Agrobiotech","ror":"https://ror.org/04vj6zn89","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I201841394","https://openalex.org/I4210088668","https://openalex.org/I4210096427","https://openalex.org/I4210153141"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Philippe Castagnone-Sereno","raw_affiliation_strings":["INRAE, Universit\u00e9 C\u00f4te d\u2019Azur, Institut Sophia Agrobiotech, Sophia Antipolis, France"],"raw_orcid":"https://orcid.org/0000-0003-2048-9651","affiliations":[{"raw_affiliation_string":"INRAE, Universit\u00e9 C\u00f4te d\u2019Azur, Institut Sophia Agrobiotech, Sophia Antipolis, France","institution_ids":["https://openalex.org/I201841394","https://openalex.org/I4210088668","https://openalex.org/I4210153141"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101561883","display_name":"Pierre Abad","orcid":"https://orcid.org/0000-0003-0062-3876","observed_orcids":["https://orcid.org/0000-0003-0062-3876"]},"institutions":[{"id":"https://openalex.org/I201841394","display_name":"Universit\u00e9 C\u00f4te d'Azur","ror":"https://ror.org/019tgvf94","country_code":"FR","type":"education","lineage":["https://openalex.org/I201841394"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210153141","display_name":"Institut Sophia Agrobiotech","ror":"https://ror.org/04vj6zn89","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I201841394","https://openalex.org/I4210088668","https://openalex.org/I4210096427","https://openalex.org/I4210153141"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Pierre Abad","raw_affiliation_strings":["INRAE, Universit\u00e9 C\u00f4te d\u2019Azur, Institut Sophia Agrobiotech, Sophia Antipolis, France"],"raw_orcid":"https://orcid.org/0000-0003-0062-3876","affiliations":[{"raw_affiliation_string":"INRAE, Universit\u00e9 C\u00f4te d\u2019Azur, Institut Sophia Agrobiotech, Sophia Antipolis, France","institution_ids":["https://openalex.org/I201841394","https://openalex.org/I4210088668","https://openalex.org/I4210153141"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053179632","display_name":"Cyril Van Ghelder","orcid":"https://orcid.org/0000-0001-5109-2249","observed_orcids":["https://orcid.org/0000-0001-5109-2249"]},"institutions":[{"id":"https://openalex.org/I201841394","display_name":"Universit\u00e9 C\u00f4te d'Azur","ror":"https://ror.org/019tgvf94","country_code":"FR","type":"education","lineage":["https://openalex.org/I201841394"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210153141","display_name":"Institut Sophia Agrobiotech","ror":"https://ror.org/04vj6zn89","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I201841394","https://openalex.org/I4210088668","https://openalex.org/I4210096427","https://openalex.org/I4210153141"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Cyril Van Ghelder","raw_affiliation_strings":["INRAE, Universit\u00e9 C\u00f4te d\u2019Azur, Institut Sophia Agrobiotech, Sophia Antipolis, France"],"raw_orcid":"https://orcid.org/0000-0001-5109-2249","affiliations":[{"raw_affiliation_string":"INRAE, Universit\u00e9 C\u00f4te d\u2019Azur, Institut Sophia Agrobiotech, Sophia Antipolis, France","institution_ids":["https://openalex.org/I201841394","https://openalex.org/I4210088668","https://openalex.org/I4210153141"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036519584","display_name":"\u00c9tienne Danchin","orcid":"https://orcid.org/0000-0003-4146-5608","observed_orcids":["https://orcid.org/0000-0003-4146-5608"]},"institutions":[{"id":"https://openalex.org/I201841394","display_name":"Universit\u00e9 C\u00f4te d'Azur","ror":"https://ror.org/019tgvf94","country_code":"FR","type":"education","lineage":["https://openalex.org/I201841394"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210153141","display_name":"Institut Sophia Agrobiotech","ror":"https://ror.org/04vj6zn89","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I201841394","https://openalex.org/I4210088668","https://openalex.org/I4210096427","https://openalex.org/I4210153141"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Etienne G J Danchin","raw_affiliation_strings":["INRAE, Universit\u00e9 C\u00f4te d\u2019Azur, Institut Sophia Agrobiotech, Sophia Antipolis, France"],"raw_orcid":"https://orcid.org/0000-0003-4146-5608","affiliations":[{"raw_affiliation_string":"INRAE, Universit\u00e9 C\u00f4te d\u2019Azur, Institut Sophia Agrobiotech, Sophia Antipolis, France","institution_ids":["https://openalex.org/I201841394","https://openalex.org/I4210088668","https://openalex.org/I4210153141"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5036519584"],"corresponding_institution_ids":["https://openalex.org/I201841394","https://openalex.org/I4210088668","https://openalex.org/I4210153141"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11179","display_name":"Nematode management and characterization studies","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11179","display_name":"Nematode management and characterization studies","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.0,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12858","display_name":"Plant Disease Resistance and Genetics","score":0.0,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/meloidogyne-incognita","display_name":"Meloidogyne incognita","score":1.0},{"id":"https://openalex.org/keywords/root-knot-nematode","display_name":"root-knot nematode","score":0.9890000224113464},{"id":"https://openalex.org/keywords/large-deletions","display_name":"large deletions","score":0.7239999771118164},{"id":"https://openalex.org/keywords/structural-variants","display_name":"structural variants","score":0.7269999980926514},{"id":"https://openalex.org/keywords/gene-loss","display_name":"gene loss","score":0.8659999966621399},{"id":"https://openalex.org/keywords/effector-genes","display_name":"effector genes","score":0.6340000033378601},{"id":"https://openalex.org/keywords/orphan-genes","display_name":"orphan genes","score":0.902999997138977},{"id":"https://openalex.org/keywords/downregulated-genes","display_name":"down-regulated genes","score":0.6769999861717224},{"id":"https://openalex.org/keywords/tomato","display_name":"tomato","score":0.49000000953674316},{"id":"https://openalex.org/keywords/experimental-evolution","display_name":"experimental evolution","score":0.5929999947547913},{"id":"https://openalex.org/keywords/asexual-reproduction","display_name":"asexual reproduction","score":0.5199999809265137}],"concepts":[{"id":"https://openalex.org/C60987743","wikidata":"https://www.wikidata.org/wiki/Q1460232","display_name":"Virulence","level":3,"score":0.9413999915122986},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.91839998960495},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.7210999727249146},{"id":"https://openalex.org/C2780617777","wikidata":"https://www.wikidata.org/wiki/Q628493","display_name":"Meloidogyne incognita","level":3,"score":0.6722000241279602},{"id":"https://openalex.org/C120804375","wikidata":"https://www.wikidata.org/wiki/Q587153","display_name":"Terra incognita","level":4,"score":0.6312999725341797},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6101999878883362},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5795999765396118},{"id":"https://openalex.org/C51785407","wikidata":"https://www.wikidata.org/wiki/Q2627568","display_name":"Effector","level":2,"score":0.5375000238418579},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5177000164985657},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.43050000071525574},{"id":"https://openalex.org/C139807058","wikidata":"https://www.wikidata.org/wiki/Q352374","display_name":"Adaptation (eye)","level":2,"score":0.4138000011444092},{"id":"https://openalex.org/C2778830712","wikidata":"https://www.wikidata.org/wiki/Q5185","display_name":"Nematode","level":2,"score":0.38179999589920044},{"id":"https://openalex.org/C2910387474","wikidata":"https://www.wikidata.org/wiki/Q331710","display_name":"Genetic Fitness","level":3,"score":0.3797999918460846},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.3163999915122986},{"id":"https://openalex.org/C174600577","wikidata":"https://www.wikidata.org/wiki/Q5533491","display_name":"Genome evolution","level":4,"score":0.2978000044822693},{"id":"https://openalex.org/C2776914050","wikidata":"https://www.wikidata.org/wiki/Q19597524","display_name":"Host adaptation","level":4,"score":0.28690001368522644},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.26930001378059387},{"id":"https://openalex.org/C2776207046","wikidata":"https://www.wikidata.org/wiki/Q2215256","display_name":"Root-knot nematode","level":3,"score":0.26589998602867126},{"id":"https://openalex.org/C87590526","wikidata":"https://www.wikidata.org/wiki/Q3592884","display_name":"Experimental evolution","level":3,"score":0.2587999999523163}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.09.04.749403","doi":"https://doi.org/10.64898/2026.09.04.749403","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.04.749403","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/08/2026.09.04.749403.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.09.04.749403","doi":"https://doi.org/10.64898/2026.09.04.749403","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.04.749403","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/08/2026.09.04.749403.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[{"display_name":"Zero hunger","score":0.6875,"id":"https://metadata.un.org/sdg/2"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7212029957.pdf","grobid_xml":"https://content.openalex.org/works/W7212029957.grobid-xml"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W595202221","https://openalex.org/W1552818321","https://openalex.org/W1653213478","https://openalex.org/W1941885189","https://openalex.org/W1961362103","https://openalex.org/W1981899094","https://openalex.org/W1983129442","https://openalex.org/W1993082390","https://openalex.org/W2001356769","https://openalex.org/W2002751165","https://openalex.org/W2003698058","https://openalex.org/W2024597572","https://openalex.org/W2025544983","https://openalex.org/W2029476353","https://openalex.org/W2062939672","https://openalex.org/W2088979319","https://openalex.org/W2093377011","https://openalex.org/W2101291993","https://openalex.org/W2103441770","https://openalex.org/W2110017782","https://openalex.org/W2121379534","https://openalex.org/W2124661861","https://openalex.org/W2130029642","https://openalex.org/W2131754114","https://openalex.org/W2156095709","https://openalex.org/W2162961259","https://openalex.org/W2169456326","https://openalex.org/W2179438025","https://openalex.org/W2432815617","https://openalex.org/W2621667957","https://openalex.org/W2789843538","https://openalex.org/W2799524357","https://openalex.org/W2940163581","https://openalex.org/W2951493739","https://openalex.org/W2951912016","https://openalex.org/W2954689043","https://openalex.org/W2980937470","https://openalex.org/W3013880810","https://openalex.org/W3158650780","https://openalex.org/W3215257960","https://openalex.org/W4200031146","https://openalex.org/W4230096730","https://openalex.org/W4308620795","https://openalex.org/W4309191898","https://openalex.org/W4319310830","https://openalex.org/W4388457858","https://openalex.org/W4391539878","https://openalex.org/W4396721167","https://openalex.org/W4406990223","https://openalex.org/W4412150723","https://openalex.org/W4416854326"],"related_works":["https://openalex.org/W194355368","https://openalex.org/W3193555883","https://openalex.org/W4230263631","https://openalex.org/W2086988611","https://openalex.org/W2156095709","https://openalex.org/W435009553","https://openalex.org/W2461799618","https://openalex.org/W1988518246","https://openalex.org/W29842557","https://openalex.org/W7005218020"],"abstract_inverted_index":{"Abstract":[0],"The":[1,14,166,201,210],"root-knot":[2],"nematode":[3,32],"Meloidogyne":[4],"incognita":[5,63,76,98,226],"is":[6,51],"a":[7],"major":[8],"constraint":[9],"to":[10,26,102,219,227],"crop":[11,56],"production":[12],"worldwide.":[13],"resistance":[15,49,82],"gene":[16],"Mi":[17,36,228],"-1.2":[18],"has":[19],"been":[20,180],"widely":[21],"deployed":[22],"in":[23,42,83,93,121,123,134,150,178,182,196,247],"tomato":[24],"varieties":[25],"control":[27],"this":[28],"parasite.":[29],"However,":[30],"virulent":[31,74,96,125,152,184,199],"isolates,":[33,65,99],"overcoming":[34],"the":[35,45,88,94,109,143,193,197,221,240],"-1.2-mediated":[37,229],"resistance,":[38],"have":[39,70,177],"increasingly":[40],"emerged":[41],"fields.":[43],"Understanding":[44],"genetic":[46],"mechanisms":[47],"underlying":[48],"circumvention":[50],"therefore":[52],"essential":[53],"towards":[54],"sustainable":[55],"protection.":[57],"From":[58],"two":[59,73,95,135,156,167,194,198],"geographically":[60],"distinct":[61],"M.":[62,75,97,225],"avirulent":[64,104],"previous":[66],"experimental":[67],"evolution":[68],"assays":[69],"allowed":[71],"producing":[72],"isolates":[77,106,145],"that":[78],"escaped":[79],"Mi-":[80],"1.2":[81],"tomato.":[84],"Here,":[85],"we":[86],"investigated":[87],"transcriptomic":[89,113],"and":[90,163,189,207],"genomic":[91],"changes":[92],"as":[100,237],"compared":[101],"their":[103],"progenitor":[105],"controlled":[107],"by":[108],"resistance.":[110,230],"First,":[111],"our":[112],"analyses":[114],"revealed":[115,146],"hundreds":[116],"of":[117,128,142,172,224,239,244],"strongly":[118],"downregulated":[119,130,173],"genes,":[120,174],"common,":[122],"both":[124,151,183],"isolates.":[126,153,185,200],"Most":[127],"these":[129,248],"genes":[131],"are":[132,217],"clustered":[133],"main":[136],"genome":[137,187,234],"regions.":[138],"Long-read":[139],"whole-genome":[140],"sequencing":[141,188],"four":[144],"parallel":[147,211],"structural":[148,213,235],"variations":[149,214],"This":[154],"included":[155],"large":[157],"deletions":[158,169,195],"spanning":[159],"ca.":[160],"1.3":[161],"Mb":[162],"0.6":[164],"Mb.":[165],"big":[168],"encompass":[170],"clusters":[171],"suggesting":[175],"they":[176],"fact":[179],"lost":[181],"Short-read":[186],"PCR":[190],"validation":[191],"confirmed":[192],"largest":[202],"deletion":[203],"includes":[204],"predicted":[205],"effector":[206],"orphan":[208],"genes.":[209],"large-scale":[212],"identified":[215],"here":[216],"likely":[218],"underlie":[220],"rapid":[222],"adaptation":[223],"These":[231],"findings":[232],"highlight":[233],"plasticity":[236],"one":[238],"potential":[241],"key":[242],"drivers":[243],"virulence":[245],"acquisition":[246],"asexually":[249],"reproducing":[250],"parasites.":[251]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-09-10T00:00:00"}
