Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel

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• dc.contributor.author Gerdol, Marco
• dc.contributor.author Cruz, Fernando
• dc.contributor.author Gómez-Garrido, Jèssica
• dc.contributor.author Vlasova, Anna
• dc.contributor.author Naranjo Ortiz, Miguel Ángel, 1989-
• dc.contributor.author Corvelo, André
• dc.contributor.author Frias, Leonor
• dc.contributor.author Gut, Marta
• dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-
• dc.contributor.author Alioto, Tyler
• dc.contributor.author Figueras, Antonio
• dc.date.accessioned 2020-12-18T07:23:49Z
• dc.date.available 2020-12-18T07:23:49Z
• dc.date.issued 2020
• dc.description.abstract Background: The Mediterranean mussel Mytilus galloprovincialis is an ecologically and economically relevant edible marine bivalve, highly invasive and resilient to biotic and abiotic stressors causing recurrent massive mortalities in other bivalves. Although these traits have been recently linked with the maintenance of a high genetic variation within natural populations, the factors underlying the evolutionary success of this species remain unclear. Results: Here, after the assembly of a 1.28-Gb reference genome and the resequencing of 14 individuals from two independent populations, we reveal a complex pan-genomic architecture in M. galloprovincialis, with a core set of 45,000 genes plus a strikingly high number of dispensable genes (20,000) subject to presence-absence variation, which may be entirely missing in several individuals. We show that dispensable genes are associated with hemizygous genomic regions affected by structural variants, which overall account for nearly 580 Mb of DNA sequence not included in the reference genome assembly. As such, this is the first study to report the widespread occurrence of gene presence-absence variation at a whole-genome scale in the animal kingdom. Conclusions: Dispensable genes usually belong to young and recently expanded gene families enriched in survival functions, which might be the key to explain the resilience and invasiveness of this species. This unique pan-genome architecture is characterized by dispensable genes in accessory genomic regions that exceed by orders of magnitude those observed in other metazoans, including humans, and closely mirror the open pan-genomes found in prokaryotes and in a few non-metazoan eukaryotes.
• dc.description.sponsorship This work was conducted with the support of the projects AGL2011-14507-E, AGL2015-65705-R, RTI2018-095997-B-I00 (Ministerio de Ciencia, Innovación y Universidades, Spain) and INCITE 10PXIB402096PR, IN607B 2016/12 (Consellería de Economía, Emprego e Industria - GAIN, Xunta de Galicia). Antonio Figueras, Beatriz Novoa, Rebeca Moreira, Alberto Pallavicini, Marco Gerdol, Paola Venier, and Umberto Rosani are supported by the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 678589. David Posada is supported by the European Research Council, the Spanish Ministry of Economy and Competitiveness, and Xunta de Galicia. We acknowledge the support of the Spanish Ministry of Science and Innovation to the EMBL partnership, the Centro de Excelencia Severo Ochoa, the CERCA Programme/Generalitat de Catalunya, the Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III, the Generalitat de Catalunya through Departament de Salut and Departament d’Empresa i Coneixement, and the Co-financing by the Spanish Ministry of Science and Innovation with funds from the European Regional Development Fund (ERDF) corresponding to the 2014-2020 Smart Growth Operating Program
• dc.format.mimetype application/pdf
• dc.identifier.citation Gerdol M, Moreira R, Cruz F, Gómez-Garrido J, Vlasova A, Rosani U et al. Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel. Genome Biol. 2020 Nov 10; 21(1): 275. DOI: 10.1186/s13059-020-02180-3
• dc.identifier.doi http://dx.doi.org/10.1186/s13059-020-02180-3
• dc.identifier.issn 1474-7596
• dc.identifier.uri http://hdl.handle.net/10230/46081
• dc.language.iso eng
• dc.publisher BioMed Central
• dc.relation.ispartof Genome Biology. 2020 Nov 10; 21(1): 275
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/AGL2011-14507-E
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/AGL2015-65705-R
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/RTI2018-095997-B-I00
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/678589
• dc.rights © Marco Gerdol et al. 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri https://creativecommons.org/licenses/by/4.0/
• dc.subject.other Musclos
• dc.subject.other Mediterrània
• dc.subject.other Genètica
• dc.subject.other Genòmica
• dc.title Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion