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.

Gill transcriptomic analysis in fast- and slow-growing individuals of Mytilus galloprovincialis

“…In bivalves, myostatin have been suggested to have alternative functions that are related with cell development (Saina and Technau, 2009;Núñez-Acuña and Gallardo-Éscarate, 2014;Morelos et al 2015;Niu et al 2015). Insulin-like peptides have been reported to act as growth regulators of soft tissues and shell in bivalves (Taylor et al 1996;Gricourt et al 2003), and their roles in determining interindividual growth rate differences in bivalves have been recently suggested by Saavedra et al (2017), who found a significant overexpression of NOV-like protein in the gills of fastgrowing Ruditapes decussatus. Using the PROSITE tool on the highly differentially expressed genes (FC>8, FDR<0.01), we have found that, in addition to myostatin and insulin-like peptides, F individuals upregulated an epidermal growth factor-like (EGF).…”

“…These authors also found some upregulated genes involved in structural remodelling in a fast-growing phenotype in agreement with previous studies indicating protein turnover as the main determinant processes for growth heterosis. Finally, Saavedra et al (2017) concluded that a set of genes controlling tissue and organ growth processes in model organisms (named 'GCGC') displayed a minor role in determining F…”

“…Valenzuela-Miranda et al 2015 In addition to overexpressing growth-regulators, the gills of F mussels overexpressed genes involved in the structure and functionality of the extracellular matrix (ECM), such as collagen, laminin, fibulin and decorin. Some of these genes have been previously reported to be differentially expressed between fast-and slow-growing individuals of different invertebrates: For instance, collagen, has been found to be upregulated in F individuals in abalones (Valenzuela-Miranda et al 2015) and clams (Saavedra et al 2017). Genomic (Zhang et al 2012) and transcriptomic (Zhao et al 2012) analyses have suggested that collagen might play an important role in shell formation and soft tissue growth and repair in bivalves.…”

“…Previous approaches to the characterization of genetic differences between fast-and slow-growing individuals of different species have emphasized the importance of differential aspects of the energetic metabolism between growth lines. For instance, Meyer and Manahan (2010) found ATP-synthase and two different NADH dehydrogenase subunits upregulated in F individuals of the oyster C. gigas, Wilson et al (2016) found fatty acid synthase like-1 and fatty acid synthase like-2 genes upregulated in fast-growing individuals of M. arenaria, and Saavedra et al (2017) ACCEPTED MANUSCRIPT…”

Nature more than nurture affects the growth rate of mussels

“…Growth is a complex phenotypic trait likely controlled by several genetic factors. Not surprisingly, gene expression rates obtained from transcriptomic analysis have shown that fast (F) and slow (S) growing specimens differ in the expression of large amounts (up to thousands) of genes involved in many biological functions [14][15][16][17] .…”