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

  • Gerdol, Marco1
  • Moreira, Rebeca2
  • Cruz, Fernando3
  • Gómez-Garrido, Jessica3
  • Vlasova, Anna4
  • Rosani, Umberto5
  • Venier, Paola5
  • Naranjo-Ortiz, Miguel A.4, 6
  • Murgarella, Maria7
  • Greco, Samuele1
  • Balseiro, Pablo2, 8
  • Corvelo, André3, 9
  • Frias, Leonor3
  • Gut, Marta3
  • Gabaldón, Toni4, 6, 10, 11
  • Pallavicini, Alberto1, 12
  • Canchaya, Carlos7, 7, 13
  • Novoa, Beatriz2
  • Alioto, Tyler S.3, 6
  • Posada, David7, 7, 13
  • And 1 more
  • 1 Università degli Studi di Trieste, Via Licio Giorgieri 5, Trieste, 34127, Italy , Trieste (Italy)
  • 2 Instituto de Investigaciones Marinas (IIM - CSIC), Eduardo Cabello, 6, Vigo, 36208, Spain , Vigo (Spain)
  • 3 Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona, 08028, Spain , Barcelona (Spain)
  • 4 CRG - Centre for Genomic Regulation, Doctor Aiguader, 88, Barcelona, 08003, Spain , Barcelona (Spain)
  • 5 Università degli Studi di Padova, Via Ugo Bassi 58/B, Padova, 35131, Italy , Padova (Italy)
  • 6 Universitat Pompeu Fabra (UPF), Barcelona, 08003, Spain , Barcelona (Spain)
  • 7 University of Vigo, Vigo, 36310, Spain , Vigo (Spain)
  • 8 Norce Norwegian Research Centre AS, Bergen, Norway , Bergen (Norway)
  • 9 New York Genome Center, New York, NY, 10013, USA , New York (United States)
  • 10 ICREA, Pg. Lluís Companys 23, Barcelona, 08010, Spain , Barcelona (Spain)
  • 11 Current address: Barelona Supercomputing Centre (BSC-CNS) and Institute for Research in Biomedicine (IRB), Barcelona, 08034, Spain , Barcelona (Spain)
  • 12 Anton Dohrn Zoological Station, 80121 Villa Comunale, Naples, Italy , Naples (Italy)
  • 13 Galicia Sur Health Research Institute, Vigo, 36310, Spain , Vigo (Spain)
Published Article
Publication Date
Nov 10, 2020
DOI: 10.1186/s13059-020-02180-3
Springer Nature


BackgroundThe 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.ResultsHere, 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.ConclusionsDispensable 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.

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