Comparative transcriptomic and proteomic analysis of yellow shell and black shell pearl oysters, Pinctada fucata martensii

Abstract

Background The pearl oyster Pinctada fucata martensii ( Pfu. ), widely cultured in the South China Sea, is a precious source of sea pearls and calcifying materials. A yellow shell variety of Pfu. was obtained after years of artificial breeding. To identify differentially expressed genes between yellow shell and normal black shell pearl oysters, we performed transcriptomic sequencing and proteomic analyses using mantle edge tissues. Results A total of 56,969 unigenes were obtained from transcriptomic, of which 21,610 were annotated, including 385 annotated significant up-regulated genes and 227 significant down-regulated genes in yellow shell oysters (| log 2 (fold change) | ≥2 and false discovery rate < 0.001). Tyrosine metabolism, calcium signalling pathway, phototransduction, melanogenesis pathways and rhodopsin related Gene Ontology (GO) terms were enriched with significant differentially expressed genes (DEGs) in transcriptomic. Proteomic sequencing identified 1769 proteins, of which 51 were significantly differentially expressed in yellow shell oysters. Calmodulin, N66 matrix protein, nacre protein and Kazal-type serine protease inhibitor were up-regulated in yellow shell oysters at both mRNA and protein levels, while glycine-rich protein shematrin-2 , mantle gene 4, and sulphide: quinone oxidoreductase were down-regulated at two omics levels. Particularly, calmodulin, nacre protein N16.3, mantle gene 4, sulphide: quinone oxidoreductase, tyrosinase-like protein 3, cytochrome P450 3A were confirmed by quantitative real-time PCR. Yellow shell oysters possessed higher total carotenoid content (TCC) compared than black shell oyster based on spectrophotography. Conclusions The yellow phenotype of pearl oysters, characterised by higher total carotenoids content, may reflect differences in retinal and rhodopsin metabolism, melanogenesis, calcium signalling pathway and biomineralisation. These results provide insights for exploring the relationships between calcium regulation, biomineralisation and yellow shell colour pigmentation. Electronic supplementary material The online version of this article (10.1186/s12864-019-5807-x) contains supplementary material, which is available to authorized users.

Evaluation of Small Molecular Polypeptides from the Mantle of Pinctada Martensii on Promoting Skin Wound Healing in Mice

“…Another study found that hydrophobic amino acids were closely related to immunological activity [17]. At the same time, another study found that the mantle of Pinctada martensii contains a relatively rich total carotenoid content, which is also related to immunity [18]. This provides a nutritional and theoretical basis for SMPs to improve immunity during the inflammatory phase of skin wound healing and to produce an inflammatory response.…”

“…At the same time, during wound healing, proteins are being continuously synthesized, thus close attention towards nitrogen balance is required. SMPs, which are rich in glutamic acid, glycine (in pearl oyster mantle edge tissue, the most highly expressed genes had glycine-rich protein [18]), cysteine, and phenylalanine can achieve this nitrogen balance that is beneficial to angiogenesis, fibroblast proliferation, collagen synthesis, and wound remodeling [19]. Normal health and physiological functions require at least 20 vitamins and at least 16 minerals and trace elements [14].…”

Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest stages using multiple whole transcriptome sequencing

“…Tyrosinases are, for example, essential in the melanogenesis pathway as key regulators of melanin biosynthesis [ 33 ]. Tyrosinase deregulation has been reported in the bivalves C. gigas , P. yessoensis and P. fucata martensii, which show contrasting pigmentation phenotypes [ 13 , 34 , 35 ]. In bivalve molluscs, mantle tissue secretes proteins responsible for shell calcification and pigmentation, and pigments are probably formed in the secretory cells in the mantle and incorporated into the shell along the growing edge [ 35 ].…”

How cultured pearls acquire their colour

“…Also these genes are involved in regulating all the other factors that regulate the colour of the nacre such as shell pigments and metal ions synthesis. In P. fucata , genes regulating calcium signalling, melanogenesis, phototransduction, rhodopsin metabolism and biomineralization was differentially expressed in the black and yellow phenotypes (Xu et al., 2019). In H. cumingii , genes related to the colour formation of the nacre layer, such as HcGIFLP1, HcCA2, HcCUBDC and Hc‐GIFLP2, were also identified (Luo, 2015).…”

“…Several multi‐omics studies have recently investigated molecular control of the production of coloured pearls with genes and transcription factors reported (Figure 2) and selective breeding processes to culture pearls of high economic value among others identified (Iwai et al, 2018; Ky et al., 2019; Xu, Huang, Shi, Zhang, & He, 2019). Although freshwater pearl productions are more suitable for studying pearl colour formation due to the longer pearl formation period than sea water pearls, this review combines both fresh and sea water pearls to provide a general overview and understanding for pearl colour formation.…”