Transcriptome characterization of the common cockle (Cerastoderma edule) after exposure to aMarteilia cochilliaoutbreak

Abstract

The edible cockle (Cerastoderma edule) is a widely cultivated bivalve with relevant ecological value roles and high value for shellfisheries in different European regions. The emergence of new threats, such as the parasiteMarteilia cochillia, has impaired the production and ecosystem of shellfish beds where the parasite was detected. Knowledge of the molecular mechanisms involved in cockle immune response to this parasite is essential to devise strategies for its control. With this aim, a transcriptomic study of the digestive gland (target organ of the parasite) and the whole cockle meat in response toM. cochilliainfection was carried out in heavily impacted area in the Northwest of Spain (Lombos do Ulla, Ria de Arousa). A total of 2079 million raw RNA-seq reads were obtained after filtering and used for annotation of 9049 genes following a conservative bioinformatic pipeline using the chromosome-level cockle genome as reference. Gene expression analysis identified a total of 973 consistent differentially expressed genes (DEGs) between comparisons across a temporal series involving cockles with different degrees of infection. DEGs increased with the level of infection within each temporal sample, but the higher DEGs number were detected when comparing temporal samples. Enrichment analysis of DEGs showed an increased expression of molecular functions related to hydrolase, peptidase activity, carbohydrate binding and active transmembrane transporter activity; cellular components such as extracellular matrix and extracellular regions; and a few biological functions associated with immunity and defence response. This information will be valuable for further studies focused on DEGs and associated SNP markers to develop reliant cockle strains to marteiliosis.

A common garden experiment supports a genetic component underlying the increased resilience of common cockle (Cerastoderma edule) to the parasite Marteilia cochillia

“…A previous genome scan in common cockle identified a set of 233 candidate SNP markers associated with resilience to marteiliosis using population genomics and transcriptomics approaches in samples with different degree of infection or exposure status collected in Ría de Arousa (Pampín et al, 2023). A total of 45 SNPs were selected as the most confident markers: 12 showing signals of divergent selection from 9154 2b‐RAD genotyped SNPs (Vera et al, 2022), and 33 associated with differentially expressed genes (DEG) through RNAseq from the enriched digestive gland transcriptome (Pardo et al, 2022). However, their application for disease management and breeding programs requires their technical validation as well as checking their ability to discriminate resilient and susceptible phenotypes.…”