mRNA-Seq and microarray development for the Grooved carpet shell clam, Ruditapes decussatus: a functional approach to unravel host -parasite interaction

Abstract

BackgroundThe Grooved Carpet shell clam Ruditapes decussatus is the autochthonous European clam and the most appreciated from a gastronomic and economic point of view. The production is in decline due to several factors such as Perkinsiosis and habitat invasion and competition by the introduced exotic species, the manila clam Ruditapes philippinarum. After we sequenced R. decussatus transcriptome we have designed an oligo microarray capable of contributing to provide some clues on molecular response of the clam to Perkinsiosis.ResultsA database consisting of 41,119 unique transcripts was constructed, of which 12,479 (30.3%) were annotated by similarity. An oligo-DNA microarray platform was then designed and applied to profile gene expression in R. decussatus heavily infected by Perkinsus olseni. Functional annotation of differentially expressed genes between those two conditionswas performed by gene set enrichment analysis. As expected, microarrays unveil genes related with stress/infectious agents such as hydrolases, proteases and others. The extensive role of innate immune system was also analyzed and effect of parasitosis upon expression of important molecules such as lectins reviewed.ConclusionsThis study represents a first attempt to characterize Ruditapes decussatus transcriptome, an important marine resource for the European aquaculture. The trancriptome sequencing and consequent annotation will increase the available tools and resources for this specie, introducing the possibility of high throughput experiments such as microarrays analysis. In this specific case microarray approach was used to unveil some important aspects of host-parasite interaction between the Carpet shell clam and Perkinsus, two non-model species, highlighting some genes associated with this interaction. Ample information was obtained to identify biological processes significantly enriched among differentially expressed genes in Perkinsus infected versus non-infected gills. An overview on the genes related with the immune system on R. decussatus transcriptome is also reported.

Monitoring nearshore ecosystem health using Pacific razor clams (Siliqua patula) as an indicator species

“…The transcript panel utilized here was developed based on studies of clams subjected to single or multiple stressors. Genes were selected for the transcript panel based on their known responses to stressors, including pathogens, xenobiotics, ocean acidification, heat stress and dissolved oxygen levels (Choi et al, 2006;Choi, Jo & Choi, 2008;Cellura, Toubiana & Roch, 2007;Gao et al, 2007;Perrigault, Tanguy & Allam, 2009;Li et al, 2011;Chen et al, 2012;Niu et al, 2013;Leite et al, 2013;Wang et al, 2013).…”

“…Calmodulin (CaM) Shell formation-indication of ocean acidification; metabolism, immune response (Chen et al, 2012;Leite et al, 2013) Ferritin (Ferr) Increased in response to pathogens, metabolizing iron (Li et al, 2011;Perrigault, Tanguy & Allam, 2009) Heat shock Protein 70 (HSP70) Thermal stress; bacteria exposure (Cellura, Toubiana & Roch, 2007) Heat shock Protein 90 (HSP90) Responds to contaminants; temperature, salinity change, metabolism; provides cellular protection (Choi et al, 2006;Choi, Jo & Choi, 2008;Gao et al, 2007).…”

Comparative immunogenomics of molluscs

“…Several microarray platforms have been designed and applied to study immunity in gastropods and bivalves of medical or aquaculture relevance (De Zoysa et al, 2012, 2011; Dheilly et al, 2011; Fleury and Huvet, 2012; Jenny et al, 2007; Leite et al, 2013; Romero et al, 2015; Venier et al, 2011; Wang et al, 2016, 2010; Zhang et al, 2016). The number of gene targets included on initial microarray designs was limited by the modest extent of available sequence data but recent microarrays can harbor upward of 30,000 gene features such that immune sequences are likely included, even if these were not specifically selected as targets on the array.…”

Understanding the cephalopod immune system based on functional and molecular evidence

“…The glutation s-transferase is also an antioxidant needed to protect the host cells from oxidative burst and it was found down-regulated. In addition, genes related to the cytoskeleton were up-regulated, suggesting a high necessity for entrap microorganisms [105].…”