Blue mussels of the Mytilus edulis species complex from South America: The application of species delimitation models to DNA sequence variation

A chromosome-scale Mytilus edulis genome assembly for aquaculture, marine ecology, and evolution

The smooth-shelled blue mussel, Mytilus edulis is part of the Mytilus species complex, encompassing at least three putative species: M. edulis, Mytilus galloprovincialis, and Mytilus trossulus. These three species occur on both sides of the Atlantic and hybridize in nature, and both M. edulis and M. galloprovincialis are important aquaculture species. They are also invasive species in many parts of the world. Here, we present a chromosome-level assembly of M. edulis. We used a combination of PacBio sequencing and Dovetail's Omni-C technology to generate an assembly with 14 long scaffolds containing 94% of the predicted length of the M. edulis genome (1.6 out of 1.7 Gb). Assembly statistics were as follows: total length = 1.65 Gb, N50 = 116 Mb, L50 = 7, and L90 = 13. BUSCO analysis showed 92.55% eukaryote BUSCOs identified. AB-Initio annotation using RNA-seq from mantle, gills, muscle, and foot predicted 47,128 genes. These gene models were combined with IsoSeq validation resulting in 45,379 full CDS protein sequences and 129,708 isoforms. Using GBS and shotgun sequencing, we also sequenced several eastern Canadian populations of Mytilus to characterize single-nucleotide as well as structural variance. This high-quality genome for M. edulis provides a platform to develop tools that can be used in breeding, molecular ecology and evolution to address questions of both commercial and environmental perspectives.

Identification and expression analysis of two steamer-like retrotransposons in the Chilean blue mussel (Mytilus chilensis)

BACKGROUND

Disseminated neoplasia (DN) is a proliferative cell disorder of the circulatory system of bivalve mollusks. The disease is transmitted between individuals and can also be induced by external chemical agents such as bromodeoxyuridine. In Mya arenaria, we have cloned and characterized an LTR-retrotransposon named Steamer. Steamer mRNA levels and gene copy number correlates with DN and can be used as a marker of the disease. So far, the only mollusk where a retrotransposon expression relates to DN is Mya arenaria. On the other hand, it has been reported that the Chilean blue mussel Mytilus chilensis can also suffers DN. Our aim was to identify retrotransposons in Mytilus chilensis and to study their expression levels in the context of disseminated neoplasia.

RESULTS

Here we show that 7.1% of individuals collected in August 2018, from two farming areas, presents morphological characteristics described in DN. Using Steamer sequence to interrogate the transcriptome of M. chilensis we found two putative retrotransposons, named Steamer-like elements (MchSLEs). MchSLEs are present in the genome of M. chilensis and MchSLE1 is indeed an LTR-retrotransposon. Neither expression, nor copy number of the reported MchSLEs correlate with DN status but both are expressed at different levels among individual animals. We also report that in cultured M. chilensis haemocytes MchSLEs1 expression can be induced by bromodeoxyuridine.

CONCLUSIONS

We conclude that SLEs present in Mytilus chilensis are differentially expressed among individuals and do not correlate with disseminated neoplasia. Treatment of haemocytes with a stressor like bromodeoxyuridine induces expression of MchSLE1 suggesting that in Mytilus chilensis environmental stressors can induce activation of LTR-retrotransposon.

Shedding light on variation in reproductive success through studies of population genetic structure in a Southeast Pacific Coast mussel

Phylogeography often focuses on the spatial dimension of genetic diversity, rarely including the temporal dynamics occurring interannually among local populations, which can provide insight into past variations in reproductive success. Currently, there is an intense aquaculture industry of Mytilus spp. on the Southeast Pacific Coast which depends entirely on the spat released by natural populations forming a relevant and sensitive social-ecological system. Temporal and spatial spat variability from natural mussel beds could be related to interannual reproductive dynamics with variable reproductive success and recruitment, which leave genetic signatures. Temporal and spatial genetic structure was evaluated in six natural beds in the Southeast Pacific (from 39°25'S to 43°07'S) on the most abundant and widespread Mytilus lineage detected, Mytilus cf. chilensis, in 4 consecutive years. Analyses included data from >180 individuals per year, with a total of 751 (mitochondrial COI) and 747 (nuclear H1) individuals, respectively. Overall, both markers showed high haplotype diversity and low spatial and temporal genetic differentiation. Likely, the high dispersal capacity of Mytilus cf. chilensis maintains population homogeneity and prevents diversity erosion. The slight differences in genetic variance of COI were better explained by differences among sites (space), and conversely, the H1 genetic variance was better explained by interannual (temporal) comparisons, which could explain temporal variability in spat availability. This study highlights the important insights achieved with the evaluation of both temporal and spatial population genetic structures in marine species with high reproductive output, which can condition the success and sustainability of the relevant social-ecological system.

SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP-array

Blue mussels from the genus Mytilus are an abundant component of the benthic community, found in the high latitude habitats. These foundation species are relevant to the aquaculture industry, with over 2 million tonnes produced globally each year. Mussels withstand a wide range of environmental conditions and species from the Mytilus edulis complex readily hybridize in regions where their distributions overlap. Significant effort has been made to investigate the consequences of environmental stress on mussel physiology, reproductive isolation, and local adaptation. Yet our understanding on the genomic mechanisms underlying such processes remains limited. In this study, we developed a multi species medium-density 60 K SNP-array including four species of the Mytilus genus. SNPs included in the platform were called from 138 mussels from 23 globally distributed mussel populations, sequenced using a whole-genome low coverage approach. The array contains polymorphic SNPs which capture the genetic diversity present in mussel populations thriving across a gradient of environmental conditions (~59 K SNPs) and a set of published and validated SNPs informative for species identification and for diagnosis of transmissible cancer (610 SNPs). The array will allow the consistent genotyping of individuals, facilitating the investigation of ecological and evolutionary processes in these taxa. The applications of this array extend to shellfish aquaculture, contributing to the optimization of this industry via genomic selection of blue mussels, parentage assignment, inbreeding assessment and traceability. Further applications such as genome wide association studies (GWAS) for key production traits and those related to environmental resilience are especially relevant to safeguard aquaculture production under climate change.

First insight into the development of a new transcriptomic tool in French Corsica harbors

Coastal harbor areas are subjected to a myriad of contamination sources with largely unknown effects. Such complex chemical mixtures are difficult to monitor but transcriptomics is a promising approach for such biomonitoring. The present study was designed to verify the use of the Coastal Biosensor for Endocrine Disruption (C-BED) assay, previously developed to detect emerging contaminants and their effects on Mytilus edulis, on another mussel species, Mytilus galloprovincialis. Mussels were caged on St-Florent harbor (contaminated) and on Revellata Bay (reference) for three months. A classical multibiomarkers approach was coupled to the C-BED assay. The results of both approaches were analysed using the Integrated Biomarkers Responses (IBR) and compared to each other. Both approaches demonstrated a higher contamination and probable endocrine disruption of mussels in St-Florent, compared to the reference station. These results confirm that the C-BED assay provides an innovative method to expand our ability to detect emerging contaminants.