Identification of genes associated with shell color in the black-lipped pearl oyster, Pinctada margaritifera

Abstract

Background: Color polymorphism in the nacre of pteriomorphian bivalves is of great interest for the pearl culture industry. The nacreous layer of the Polynesian black-lipped pearl oyster Pinctada margaritifera exhibits a large array of color variation among individuals including reflections of blue, green, yellow and pink in all possible gradients. Although the heritability of nacre color variation patterns has been demonstrated by experimental crossing, little is known about the genes involved in these patterns. In this study, we identify a set of genes differentially expressed among extreme color phenotypes of P. margaritifera using a suppressive and subtractive hybridization (SSH) method comparing black phenotypes with full and half albino individuals.

Results: Out of the 358 and 346 expressed sequence tags (ESTs) obtained by conducting two SSH libraries respectively, the expression patterns of 37 genes were tested with a real-time quantitative PCR (RT-qPCR) approach by pooling five individuals of each phenotype. The expression of 11 genes was subsequently estimated for each individual in order to detect inter-individual variation. Our results suggest that the color of the nacre is partially under the influence of genes involved in the biomineralization of the calcitic layer. A few genes involved in the formation of the aragonite tablets of the nacre layer and in the biosynthesis chain of melanin also showed differential expression patterns. Finally, high variability in gene expression levels were observed within the black phenotypes.

Conclusions: Our results revealed that three main genetic processes were involved in color polymorphisms: the biomineralization of the nacreous and calcitic layers and the synthesis of pigments such as melanin, suggesting that color polymorphism takes place at different levels in the shell structure. The high variability of gene expression found within black phenotypes suggests that the present work should serve as a basis for future studies exploring more thoroughly the expression patterns of candidate genes within black phenotypes with different dominant iridescent colors.

Fig. 1

Picture of dissected specimens of Pinctada margaritifera of the three studied phenotypes. a. Full albino (FA; white shell and white mantle), b. half albino (HA; white shell and black mantle), c. black phenotype (C; black shell and black mantle)

Fig. 2

TreeMap visualization of the summary of GO Molecular function found for the black phenotypes, obtained with a Revigo analysis. The size of each boxe is correlated to the frequencies of the occurence of the GO-term. Boxes with the same color are grouped by semantic similarity (SimRel, similarity = 0.7) and correspond to the same upper-hierarchy GO-term which is found in grey in the middle of each box

Fig. 3

TreeMap visualization of the summary of GO Molecular function found for the full albinos phenotypes obtained with a Revigo analysis. The size of each boxe is correlated to the frequencies of the occurence of the GO-term. Boxes with the same color are grouped by semantic similarity (SimRel, similarity = 0.7) and correspond to the same upper-hierarchy GO-term which is found in grey in the middle of each box

Fig. 4

Relative gene expression levels obtained with the pooled analysis. For each tested gene, the white histogram represents the expression in the full albino phenotype (FA), the grey histogram in the half albino (HA) and the black histogram in the black phenotype (C). TYR2a and TYR2c are 2 fragments of the same gene coding for Tyrosinase. Significant differential expressions (>2 folds) in phenotypes (FA) and (HA) relative to phenotype (C) are indicated by a red star

Fig. 5

Relative gene expression levels obtained with the individual analysis. For each tested gene, the white histogram represents the expression in the full albino phenotype (FA), the grey histogram in the half albino (HA) and the black histogram in the black phenotype (C). Significant differential expressions in phenotypes (FA) and (HA) relative to phenotype (C) (determined by an ANOVA) are indicated by a red star