Integration of Next Generation Sequencing and EPR Analysis to Uncover Molecular Mechanism Underlying Shell Color Variation in Scallops

Abstract

The Yesso scallop Patinopecten yessoensis displays polymorphism in shell colors, which is of great interest for the scallop industry. To identify genes involved in the shell coloration, in the present study, we investigate the transcriptome differences by Illumina digital gene expression (DGE) analysis in two extreme color phenotypes, Red and White. Illumina sequencing yields a total of 62,715,364 clean sequence reads, and more than 85% reads are mapped into our previously sequenced transcriptome. There are 25 significantly differentially expressed genes between Red and White scallops. EPR (Electron paramagnetic resonance) analysis has identified EPR spectra of pheomelanin and eumelanin in the red shells, but not in the white shells. Compared to the Red scallops, the White scallops have relatively higher mRNA expression in tyrosinase genes, but lower expression in other melanogensis-associated genes. Meantime, the relatively lower tyrosinase protein and decreased tyrosinase activity in White scallops are suggested to be associated with the lack of melanin in the white shells. Our findings highlight the functional roles of melanogensis-associated genes in the melanization process of scallop shells, and shed new lights on the transcriptional and post-transcriptional mechanisms in the regulation of tyrosinase activity during the process of melanin synthesis. The present results will assist our molecular understanding of melanin synthesis underlying shell color polymorphism in scallops, as well as other bivalves, and also help the color-based breeding in shellfish aquaculture.

Transcriptional profiling of long non-coding RNAs in mantle of Crassostrea gigas and their association with shell pigmentation

“…At present, the main shell pigments found in Mollusca are carotenoids, melanin and tetrapyrroles, including porphyrins and bile pigments 11 , 18 . The molecular processes involved in the synthesis of pigment have been studied in only a few molluscs 19 – 24 . Of that, the regulatory mechanism for melanin synthesis is better known in cephalopods, involving in the activation of tyrosinase and increased melanin synthesis in the ink gland 25 .…”

Differences between fast and slow muscles in scallops revealed through proteomics and transcriptomics

“…Our current knowledge on muscle specific proteins in scallops has been established primarily by traditional biochemical and immunohistochemical techniques, which require laborious work and yield a limited number of enzymes or proteins [ 10 ]. Recently, the advances in iTRAQ (isobaric tags for relative and absolute quantitation) proteomics and RNA-Seq transcriptomics enable us to identify and quantify thousands of genes and proteins in a single experiment [ 3 , 29 – 31 ]. Here, we performed the first, integrated proteomic and transcriptomic analyses of differences between the fast (striated) and slow (catch) adductor muscles in Yesso scallop ( Patinopecten yessoensis ; Fig.…”

A Genome-Wide Association Study Identifies Candidate Genes Associated With Shell Color in Bay Scallop Argopecten irradians irradians

“…Furthermore, transcriptomes and digital gene expression analysis of four different color clams, Meretrix meretrix, suggested that several potential genes and the Notch pathway played a crucial role in its shell color patterning (Yue et al, 2015). The same method was also exerted in two extreme color phenotypes of Yesso scallop, Patinopecten yessoensis, and 25 significantly differential expression genes were identified for unraveling shell color differences (Sun et al, 2016). These researches provided pivotal loci/genes responsible for the formation of shell coloration and served as candidate markers for mollusks breeding projects.…”