AGS was funded by the Portuguese Foundation for Science and Technology (FCT) under the
grant SFRH/BD/137935/2018 and COVID/DB/152933/2022, which also supported MLL
(2020.03608.CEECIND) and EF (CEECINST/00027/2021). This research was developed under
the project EdgeOmics - Freshwater Bivalves at the Edge: Adaptation genomics under
climate-change scenarios (PTDC/CTA-AMB/3065/2020) funded by FCT through national
funds. Additional strategic funding was provided by FCT UIDB/04423/2020 and
UIDP/04423/2020.
Contiguous assemblies are fundamental to deciphering the composition of extant genomes. In
molluscs, this is considerably challenging owing to the large size of their genomes, heterozygosity,
and widespread repetitive content. Consequently, long-read sequencing technologies are
fundamental for high contiguity and quality. The first genome assembly of Margaritifera
margaritifera (Linnaeus, 1758) (Mollusca: Bivalvia: Unionida), a culturally relevant, widespread,
and highly threatened species of freshwater mussels, was recently generated. However, the
resulting genome is highly fragmented since the assembly relied on short-read approaches. Here,
an improved reference genome assembly was generated using a combination of PacBio CLR long
reads and Illumina paired-end short reads. This genome assembly is 2.4 Gb long, organized into
1,700 scaffolds with a contig N50 length of 3.4 Mbp. The ab initio gene prediction resulted in
48,314 protein-coding genes. Our new assembly is a substantial improvement and an essential
resource for studying this species’ unique biological and evolutionary features, helping promote
its conservation.
