Evidence of multiple genome duplication events in Mytilus evolution

Abstract

Background: Molluscs remain one significantly under-represented taxa amongst available genomic resources, despite being the second-largest animal phylum and the recent advances in genomes sequencing technologies and genome assembly techniques. With the present work, we want to contribute to the growing efforts by filling this gap, presenting a new high-quality reference genome for Mytilus edulis and investigating the evolutionary history within the Mytilidae family, in relation to other species in the class Bivalvia.

Results: Here we present, for the first time, the discovery of multiple whole genome duplication events in the Mytilidae family and, more generally, in the class Bivalvia. In addition, the calculation of evolution rates for three species of the Mytilinae subfamily sheds new light onto the taxa evolution and highlights key orthologs of interest for the study of Mytilus species divergences.

Conclusions: The reference genome presented here will enable the correct identification of molecular markers for evolutionary, population genetics, and conservation studies. Mytilidae have the capability to become a model shellfish for climate change adaptation using genome-enabled systems biology and multi-disciplinary studies of interactions between abiotic stressors, pathogen attacks, and aquaculture practises.

Keywords: Evolution; Mytilus edulis; Paleogenomics; Positive selection; Whole-genome duplication.

Fig. 1

Gene composition and annotation estimations. A BUSCO evaluation (Metazoa database; number of framework genes 954), 98.9% of the gene were recovered; B A five-way Venn diagram. The figure shows the unique and common genes displaying predicted protein sequence similarity with one or more databases (details in Supplementary Table S3); C Level 2 GO annotations using the gene ontology of assembled transcripts

Fig. 2

Genome assembly. A M. edulis annotated mitochondrial genome; B Phylogenetic tree inferred from the mitochondrial gene

Fig. 3

Ka and Ks analysis. A Distribution of the Ks values of the duplicate pairs in M. coruscus, M. edulis and M. galloprovincialis; B Bivalvia (class) ortholog Ks distribution and multiple WGDs. Combined Ks plot of the gene age distributions of seven species (see Tables S5 and S6). The median peaks for these plots are highlighted. Analyses of ortholog divergence indicated that these taxa diverged after their most recent WGDs

Fig. 4

Mean Ka/Ks ratios for each orthologs cluster in the A M. edulis and M. galloprovincialis; B M. edulis and M. coruscus; C M. coruscus and M. galloprovincialis