Transcriptome characterization of the common cockle ( Cerastoderma edule ) after exposure to a Marteilia cochillia outbreak

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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 parasite Marteilia 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 to M. cochillia infection 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.

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