Hybrid de novo assembly of the draft genome of the freshwater mussel Venustaconcha ellipsiformis (Bivalvia: Unionida)

Abstract

Freshwater mussels (Bivalvia: Unionida) serve an important role as aquatic ecosystem engineers but are one of the most critically imperilled groups of animals. An assembled and annotated genome for freshwater mussels has the potential to be utilized as a valuable resource for many researchers given their ecological value and threatened status. In addition, a sequenced genome will help to answer more fundamental questions of sex-determination and genome evolution in bivalves exhibiting a unique “doubly uniparental inheritance” mode of mitochondrial DNA transmission through comparative genomics approaches. Here, we used a combination of sequencing strategies to assemble and annotate a draft genome of the freshwater mussel Venustaconcha ellipsiformis. The genome described here was obtained by combining high coverage short reads (65X genome coverage of Illumina paired-end and 11X genome coverage of mate-pairs sequences) with low coverage Pacific Biosciences long reads (0.3X genome coverage). Briefly, the final scaffold assembly accounted for a total size of 1.54Gb (366,926 scaffolds, N50 = 6.5Kb, with 2.3% of "N" nucleotides), representing 93% of the predicted genome size of 1.66Gb. Over one third of the genome (37.5%) consisted of repeated elements and more than 85% of the core eukaryotic genes were recovered. Finally, we reassembled the full mitochondrial genome and found six polymorphic sites with respect to the previously published reference. This resource opens the way to comparative genomics studies to identify genes related to the unique adaptations of freshwater mussels and their distinctive mitochondrial inheritance mechanism.