High quality genome for the threatened Louisiana Pearlshell Margaritifera hembeli (Conrad, 1838)

Samantha A Donohoo, Nathan V Whelan. Journal of Molluscan Studies, Volume 92, Issue 3, September 2026, eyag016, DOI: 10.1093/mollus/eyag016

Abstract

The order Unionida, known as freshwater mussels, are a highly diverse group with more than 1,000 species found throughout the world’s freshwater systems. These species display unique adaptations such as an unusual mitochondrial inheritance system and a parasitic larval stage that can infect freshwater fish and various species of amphibians. To date there are nine published genomes for the order Unionida, with only two genomes from North American species and only one genome for the widely-distributed genus Margaritifera. Here we present the first genome assembly and annotation for Margaritifera hembeli, a federally threatened species in the USA, produced from a combination of PacBio HiFi long-reads, Illumina paired-end short-reads and RNA sequencing of three tissue types. The high-quality genome was assembled by combining the PacBio HiFi sequencing with Bionano SAPHYR optical mapping and annotated with the Funannotate pipeline. The final reference assembly is large and highly contiguous, comprising 2,176 scaffolds and 3,020,926,712 bp, with a scaffold N50 of 9,733,982 bp. The genome of M. hembeli has extremely low heterozygosity (0.07%), similar to previously published population genomics work. The genome also has the highest number of repeats (63.02%) among previously published freshwater mussel genome assemblies. Genome annotation predicted 58,805 genes, of which 24,998 were functionally annotated as protein-coding and an additional 6,090 as transfer RNAs. Finally, we characterized the homeobox gene cluster in M. hembeli and found unusual homeobox gene rearrangement that conflicts with homeobox clusters in other bivalves. We also identified genes involved in biomineralization and found two expanded gene families associated with shell matrix proteins involved in the formation of pearls and nacre. This reference genome is an important tool for conservation of freshwater mussel species.