Genome survey of the freshwater mussel Venustaconcha ellipsiformis (Bivalvia: Unionida) using a hybrid de novo assembly approach

Abstract

Freshwater mussels (Bivalvia: Unionida) serve an important role as aquatic ecosystem engineers but are one of the most critically imperilled groups of animals. Here, we used a combination of sequencing strategies to assemble and annotate a draft genome of Venustaconcha ellipsiformis, which will serve as a valuable genomic resource given the ecological value and unique “doubly uniparental inheritance” mode of mitochondrial DNA transmission of freshwater mussels. 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 86% of the predicted genome size of 1.80Gb, while over one third of the genome (37.5%) consisted of repeated elements and more than 85% of the core eukaryotic genes were recovered. Given the repeated genetic bottlenecks of V. ellipsiformis populations as a result of glaciations events, heterozygosity was also found to be remarkably low (0.6%), in contrast to most other sequenced bivalve species. 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.

Molecular characterization of AwSox2 from bivalve Anodonta woodiana: Elucidating its player in the immune response

“…Interestingly, a series of conserved genes are shared between mollusca and vertebrates, but not between arthropod and vertebrates, such as estrogen receptor, Sox, TNF, prostaglandin E synthase and others. 21 To date, only some Sox proteins have been identified and characterized in this group. [22][23][24] In gastropods, SoxB and SoxC were detected in the cerebral and pleuropedal ganglia of abalone Haliotis asinina.…”

The Gene-Rich Genome of the ScallopPecten maximus

“…Other sequenced genomes for more distantly related bivalves include those of the Sydney Rock Oyster Saccostrea glomerata [20], Eastern oyster Crassostrea virginica [unpublished, but see 21], the Snout Otter Clam Lutraria rhynchaena [22], Blood Clam Scapharca broughtonii [23] and Manila Clam Ruditapes philippinarum [24]. There are also extant resources for the mussel Mytillus galloprovincialis [25] and the freshwater mussels Venustaconcha ellipsiformis [26], Limnoperna fortunei [27], Dreissena rostriformis [28] and Dreissena polymorpha [unpublished, but see 29]. Of these resources, only the assemblies for Crassostrea virginica and Scapharca broughtonii are of chromosomal quality, and the scaffold N50 of the other resources varies widely.…”

The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

“…Unlike many other bivalves (e.g. 23,24 ), both V. ellipsiformis and M. nervosa genomes revealed relatively low levels of heterozygosity, with estimated values per site of 0.0060 and 0.0077, respectively 19,20 .…”

“…Several Mollusca genomes are currently available and new assemblies are released every year at an increasing trend (reviewed in [16][17][18] ). Despite this, to date, only two Unionida mussel genomes have been published, those of Venustaconcha ellipsiformis (Conrad, 1836) 19 and Megalonaias nervosa (Rafinesque, 1820) 20 . These represent valuable comparative resources and are among the largest bivalve genomes sequenced to date (1.80 Gb and 2.36 Gb respectively) 16,18 ; known Bivalvia genome sizes range from 0.559 Gb (Crassostrea gigas, ).…”