Analysis of Gene Expression in an Inbred Line of Soft-Shell Clams (Mya arenaria) Displaying Growth Heterosis: Regulation of Structural Genes and the NOD2 Pathway

Abstract

Mya arenaria is a bivalve mollusk of commercial and economic importance, currently impacted by ocean warming, acidification, and invasive species. In order to inform studies on the growth of M. arenaria, we selected and inbred a population of soft-shell clams for a fast-growth phenotype. This population displayed significantly faster growth (p < 0.0001), as measured by 35.4% greater shell size. To assess the biological basis of this growth heterosis, we characterized the complete transcriptomes of six individuals and identified differentially expressed genes by RNAseq. Pathways differentially expressed included structural gene pathways. Also differentially expressed was the nucleotide-binding oligomerization domain 2 (NOD2) receptor pathway that contributes to determination of growth, immunity, apoptosis, and proliferation. NOD2 pathway members that were upregulated included a subset of isoforms of RIPK2 (mean 3.3-fold increase in expression), ERK/MAPK14 (3.8-fold), JNK/MAPK8 (4.1-fold), and NFκB (4.08-fold). These transcriptomes will be useful resources for both the aquaculture community and researchers with an interest in mollusks and growth heterosis.

NOD2 maybe a biomarker for the survival of kidney cancer patients

“…In the present analysis, no enough evidence was promulgated to authenticate the existing association between NOD2 and kidney cancers. More sequencing data and studies on the mechanism of cancer occurrence and clinical trials about NOD2 gene, such as inflammation and immune disease area [ 25 , 26 ], are needed to further reveal the specific mechanism of action in kidney cancer areas.…”

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

“…Thus, the GO term findings supported the higher growth rates and activity levels of F individuals in comparison with S mussels. Not surprisingly, previous works on interindividual growth rate differences in bivalves have also described similar GO terms as the main processes underlying growth differences; for instance, Wilson et al (2016) reported that 19% of GO terms of differentially expressed genes in fast-growing Mya arenaria are associated with cell structure, whereas 17% refer to signalling and growth, 12% to energy and nutrient metabolism and 10% to DNA/RNA and protein synthesis. Regarding the KEGG terms, energetic metabolism terms were referred to F individuals in good correspondence to their higher activity levels.…”

“…More recently, De la Peña et al (2016) reported the existence of significant differences in the rate of expression of ferritins (Apfer1) between fast-and slow-growing individuals of Argopecten purpuratus at different developmental stages (5 stages from embryos to juveniles). Wilson et al (2016) produced an inbred fast growth line (F) of Mya arenaria clams and analysed the gene expression to test the hypothesis that specific growthrelated genes will be upregulated in F individuals. These authors established a positive correlation between some metabolic genes (fatty acid synthase and ATPase) with fast growth.…”

“…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…”