The genome of the zebra mussel,Dreissena polymorpha: a resource for comparative genomics, invasion genetics, and biocontrol

Abstract

The zebra mussel, Dreissena polymorpha, continues to spread from its native range in Eurasia to Europe and North America, causing billions of dollars in damage and dramatically altering invaded aquatic ecosystems. Despite these impacts, there are few genomic resources for Dreissena or related bivalves. Although the D. polymorpha genome is highly repetitive, we have used a combination of long-read sequencing and Hi-C-based scaffolding to generate a high-quality chromosome-scale genome assembly. Through comparative analysis and transcriptomics experiments we have gained insights into processes that likely control the invasive success of zebra mussels, including shell formation, synthesis of byssal threads, and thermal tolerance. We identified multiple intact Steamer-Like Elements, a retrotransposon that has been linked to transmissible cancer in marine clams. We also found that D. polymorpha have an unusual 67 kb mitochondrial genome containing numerous tandem repeats, making it the largest observed in Eumetazoa. Together these findings create a rich resource for invasive species research and control efforts.

The native mussel Mytilus chilensis genome reveals adaptative molecular signatures facing the marine environment

“…These long reads were assembled with the Hifiasm package using default parameters (Cheng et al, 2021), yielding a primary assembly of 13,762 contigs equivalent to 2.19 Gb, with an N50 of 206 Mb. The size genome assembly made by Hifiasm was comparable with the previous genome size described for closely related species; 1.28 Gb for M. galloprovincialis (Gerdol et al, 2020), 1.57 Gb for M. coruscus (Yang et al, 2021) and 1.79 Gb for Dreissena polymorpha (McCartney et al, 2022).…”

“…galloprovincialis (Gerdol et al, 2020), 1.57 Gb for M. coruscus (Yang et al, 2021) and 1.79 Gb for Dreissena polymorpha (McCartney et al, 2022).…”

“…Unfortunately, these genome features challenge the assembly efforts to avoid genome fragmentation. Up to now, chromosome-level genome assembly for Mytilidae has only been reported for the congeneric species M. coruscus (Yang et al, 2021) and for the zebra mussel Dreissena polymorpha (McCartney et al, 2022); meanwhile, other members of the Family have been reported as highly contiguous reference assemblies at contig level (Murgarella et al, 2016; Renaut et al, 2018; Xu et al, 2017). Interestingly, the presence-absence variation (PAV) phenomenon has recently been reported for M. galloprovincialis , where a pan-genome composed of 20,000 protein-coding genes was observed in conjunction with dispensable genes that are entirely missing in some mussels (Gerdol et al, 2020).…”

“…For instance, mussel species display morphologically conserved karyotypes, and there is no evidence of whole-genome duplication events (Perez-Garcia, Moran, & Pasantes, 2014). Compared with other bivalves, the reported mussel genomes share relatively large genome sizes characterized by high heterozygosity and expanded mobile elements (Du et al, 2017;McCartney et al, 2022;Uliano-Silva et al, 2017;S. Wang et al, 2017;Zhang et al, 2012).…”

A high quality chromosome-level genome assembly for the golden mussel (Limnoperna fortunei)

“…Almost half (46.93%) of the genome was annotated as repetitive sequences according to the EarlGrey pipeline [9], with 35.80% of the genome labeled as unclassified repeats (Table 2). Similarly high proportions of unclassified repeats have been reported in other mussels [10, 11]. The second most frequent repeat class detected was Long interspersed nuclear elements (LINE), representing 4.51% of the total genome.…”