A Microarray Study of Carpet-Shell Clam (Ruditapes decussatus) Shows Common and Organ-Specific Growth-Related Gene Expression Differences in Gills and Digestive Gland

Abstract

Growth rate is one of the most important traits from the point of view of individual fitness and commercial production in mollusks, but its molecular and physiological basis is poorly known. We have studied differential gene expression related to differences in growth rate in adult individuals of the commercial marine clam Ruditapes decussatus. Gene expression in the gills and the digestive gland was analyzed in 5 fast-growing and five slow-growing animals by means of an oligonucleotide microarray containing 14,003 probes. A total of 356 differentially expressed genes (DEG) were found. We tested the hypothesis that differential expression might be concentrated at the growth control gene core (GCGC), i.e., the set of genes that underlie the molecular mechanisms of genetic control of tissue and organ growth and body size, as demonstrated in model organisms. The GCGC includes the genes coding for enzymes of the insulin/insulin-like growth factor signaling pathway (IIS), enzymes of four additional signaling pathways (Raf/Ras/Mapk, Jnk, TOR, and Hippo), and transcription factors acting at the end of those pathways. Only two out of 97 GCGC genes present in the microarray showed differential expression, indicating a very little contribution of GCGC genes to growth-related differential gene expression. Forty eight DEGs were shared by both organs, with gene ontology (GO) annotations corresponding to transcription regulation, RNA splicing, sugar metabolism, protein catabolism, immunity, defense against pathogens, and fatty acid biosynthesis. GO term enrichment tests indicated that genes related to growth regulation, development and morphogenesis, extracellular matrix proteins, and proteolysis were overrepresented in the gills. In the digestive gland overrepresented GO terms referred to gene expression control through chromatin rearrangement, RAS-related small GTPases, glucolysis, and energy metabolism. These analyses suggest a relevant role of, among others, some genes related to the IIS, such as the ParaHox gene Xlox, CCAR and the CCN family of secreted proteins, in the regulation of growth in bivalves.

Keywords: bivalves; digestive gland; gills; growth rate; insulin signaling pathway; organ-specific gene expression.

Figure 1

Individual growth rate regressed onto the initial size for the clams of the experimental population (N = 40). Dots mark the individuals that were used for gene expression analysis. The regression equation is as follows: y = −0.0753x + 0.4303 (R² = 0.28).

Figure 2

Frequencies of the Molecular Function GO terms in the set of genes that showed significant (PFP < 0.15) differential expression between F and S clams in the digestive gland. The GO terms were treated with REVIGO for grouping terms with semantic similarity.

Figure 3

Frequencies of the Molecular Function GO terms in the set of genes that showed significant (PFP < 0.15) differential expression between F and S clams in the gills. The GO terms were treated with REVIGO for grouping terms with semantic similarity.

Figure 4

Frequencies of the Molecular Function GO terms in the set of genes that showed significant (PFP < 0.15) differential expression between F and S clams in both the gills and the digestive gland. The GO terms were treated with REVIGO for grouping terms with semantic similarity. The number of terms grouped are given in parenthesis when appropriate.