Uncovering the immunological repertoire of the carpet shell clam Ruditapes decussatus through a transcriptomic-based approach

Frederico M Batista,Allison M Churcher,Manuel Manchado,Alexandra Leitão,Deborah M Power

doi:10.1016/j.aaf.2018.03.003

Abstract

The grooved carpet-shell clam Ruditapes decussatus is native to the Northern Atlantic and Mediterranean Sea and has a high commercial value. It is one of the main native bivalve species cultured in Europe. The main objective of the present study was to gain further insights into the immunological repertoire of R. decussatus through a transcriptomic approach. Pooled mantle samples of eight R. decussatus individuals were sequenced using Illumina platform. A total of 67 132 contigs with more than 800 bp were obtained. Manual annotation of these contigs revealed 146 immune-related genes. The gene families in which the highest number of immune-related genes was observed were: C1q domain-containing proteins (63), tumor necrosis factors (15) and toll-like receptors (TLRs, 10). A total of 5 359 putative single nucleotide polymorphisms (SNPs) were identified in the 146 immune-related genes. The density of SNPs ranged between 0.04 and 7.92 SNPs/100 bp. The highest and the lowest SNP density were observed in genes of the C1q domain-containing protein family. Due to the importance of TLRs in innate immunity, we focused our attention on these membrane receptors. Ten TLRs were identified based on protein domain organization. Phylogenetic analysis revealed that R. decussatus TLRs were diverse and only 3 showed orthology with TLRs of known immune functions in other bivalve species. Moreover, our analysis suggests that lineage restricted-expansions of TLRs occurred in all mollusc taxa analysed including in venerids.

Highlights

Aquaculture is one of the fastest-growing food producing sectors in the world and has a high social and economic importance
We observed 3 913, 1 510 and 757 Gene Ontology (GO) functional categories belonging to biological process (BP), molecular function (MF) and cellular component (CC), respectively
These results suggest that the transcripts observed in the mantle of R. decussatus cover a wide range of biological processes

Summary

Introduction

Aquaculture is one of the fastest-growing food producing sectors in the world and has a high social and economic importance. According to the Food and Agriculture Organization (FAO, 2014), the production of mollusc bivalves represented approximately 22% of world aquaculture production. The carpet shell clam Ruditapes decussatus is one of the main native bivalve species produced in Europe, with Portugal leading production in the world with a total production of 2 320 tonnes in 2012 (FAO, 2014). Mollusc bivalves lack a specific immune response and associated immunological memory, and rely on the innate immune system. Several immune-related genes have been identified involved in the cellular and humoral innate response of bivalves, such as recognition of pathogen-associated molecular patterns, activation of signal pathways, haemocyte mediated reactions and production of immune effectors (Schmitt, Gueguen, Desmarais, Bachere, & de Lorgeril, 2010)

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