Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel
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RESEARCH
Open Access
Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel Marco Gerdol1, Rebeca Moreira2, Fernando Cruz3, Jessica Gómez-Garrido3, Anna Vlasova4, Umberto Rosani5, Paola Venier5, Miguel A. Naranjo-Ortiz4,6, Maria Murgarella7, Samuele Greco1, Pablo Balseiro2,8, André Corvelo3,9, Leonor Frias3, Marta Gut3, Toni Gabaldón4,6,10,11, Alberto Pallavicini1,12, Carlos Canchaya7,13,14, Beatriz Novoa2, Tyler S. Alioto3,6, David Posada7,13,14* and Antonio Figueras2* * Correspondence: dposada@uvigo. es; [email protected] 7 Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain 2 Instituto de Investigaciones Marinas (IIM - CSIC), Eduardo Cabello, 6, 36208 Vigo, Spain Full list of author information is available at the end of the article
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 nonmetazoan eukaryotes. Keywords: Mussel, Bivalve, Pan-genome, Presence-absence variation, Structural variants, Hemizygosity, Dispensable gene, Phylome, Innate immunity, Antimicrobial peptides
© The Author(s). 2020 Open Access 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,
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