Mussels of order Unionida are a group of strictly freshwater bivalves with nearly 1,000 described species, with a dispersed geographic distribution across the world’s freshwater ecosystems. Despite their fundamental ecological importance, they are highly threatened, being the faunal group with the highest records of wild extinctions. To date, only five freshwater mussel species have had their whole genome sequenced, of which only two are from European species. Here, we present the first genome assembly of the painter’s mussel, Unio pictorum (Linnaeus, 1758), the type species representative of the order and the most widespread species of the genus in Europe. We used long-read PacBio HiFi sequencing reads to produce a highly contiguous assembly that will pave the way for the study of European freshwater mussels in the Genome Era.

The European sardine (Sardina pilchardus, Walbaum 1792) is indisputably a commercially important species. Previous studies using uneven sampling or a limited number of makers have presented sometimes conflicting evidence for the genetic structure of S. pilchardus populations.  Here we show that whole genome data from 108 individuals from 16 sampling areas across 5,000 Km of the species’ distribution range (from the Eastern Mediterranean to the archipelago of Azores) supports at least three genetic clusters. One includes individuals from Azores and Madeira, with evidence of substructure separating these two archipelagos in the Atlantic. Another cluster broadly corresponds to the center of the distribution including the sampling sites around Iberia, separated by the Almeria-Oran front from the third cluster that includes all of the Mediterranean samples, except those from the Alboran Sea. Individuals from the Canary Islands appear as belonging to the same ancestral group as those from the Mediterranean. This suggests at least two important geographical barriers to gene flow, even though these do not seem complete, with many individuals from around Iberia and the Mediterranean showing some patterns compatible with admixture with other genetic clusters. Genomic regions corresponding to the top outliers of genetic differentiation are located in areas of low recombination indicative that genetic architecture also has a role in shaping population structure. These regions include genes related to otolith formation, a calcium carbonate structure in the inner ear previously used to distinguish S. pilchardus populations.  Our results provide a baseline for further characterization of physical and genetic barriers that divide European sardine populations, and information for transnational stock management of this highly exploited species towards sustainable fisheries.