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

Abstract

Background Albino mutations are commonly observed in the animal kingdom, including in bivalves. In the black-lipped pearl oyster Pinctada margaritifera, albino specimens are characterized by total or partial absence of colouration resulting in typical white shell phenotype expression. The relationship of shell colour with resulting cultured pearl colour is of great economic interest in P. margaritifera, on which a pearl industry is based. Hence, the albino phenotype provides a useful way to examine the molecular mechanisms underlying pigmentation. Results Whole transcriptome RNA-sequencing analysis comparing albino and black wild-type phenotypes at three stages over the culture cycle of P. margaritifera revealed a total of 1606, 798 and 187 differentially expressed genes in whole juvenile, adult mantle and pearl sac tissue, respectively. These genes were found to be involved in five main molecular pathways, tightly linked to known pigmentation pathways: melanogenesis, calcium signalling pathway, Notch signalling pathway, pigment transport and biomineralization. Additionally, significant phenotype-associated SNPs were selected (N = 159), including two located in the Pif biomineralization gene, which codes for nacre formation. Interestingly, significantly different transcript splicing was detected between juvenile (N = 1366) and adult mantle tissue (N = 313) in, e.g., the tyrosinase Tyr-1 gene, which showed more complex regulation in mantle, and the Notch1 encoding gene, which was upregulated in albino juveniles. Conclusion This multiple RNA-seq approach provided new knowledge about genes associated with the P. margaritifera albino phenotype, highlighting: 1) new molecular pathways, such as the Notch signalling pathway in pigmentation, 2) associated SNP markers with biomineraliszation gene of interest like Pif for marker-assisted selection and prevention of inbreeding, and 3) alternative gene splicing for melanin biosynthesis implicating tyrosinase.

DNA Methylation Analyses Unveil a Regulatory Landscape in the Formation of Nacre Color in Pearl Oyster Pinctada fucata martensii

“…It has been reported that biomineralization is closely related to shell pigmentation, sequential layer-by-layer mineralization is directed by cells at the edge of the mantle tissues, and pigments in the periostracum layer are produced by the mantle ( Xu et al, 2019 ). In Pinctada margaritifera , multiple transcriptome analysis supports the involvement of biomineralization genes in the process of shell pigmentation ( Auffret et al, 2020 ). The shell mineralization process involves energy metabolism and organic matrix crystallization ( Zhao et al, 2019 ; Zhao et al, 2020 ; He et al, 2021 ).…”

Evolution and Function of the Notch Signaling Pathway: An Invertebrate Perspective

“…There are studies that white-shell oysters could employ endocytosis to downregulate Notch levels and lead to melanoblasts apoptosis, preventing pigmentation [ 82 ]. In addition to this, Notch-related genes (Delta, Jagged-2, E3 ubiquitin-protein ligase) are upregulated in the albino juvenile phenotype in Pinctada margaritifera ( P. margaritifera ) [ 86 ].…”

Revealing genetic diversity, population structure, and selection signatures of the Pacific oyster in Dalian by whole-genome resequencing

“…The Notch signaling pathway, an evolutionarily conserved cell signaling system, functions in a great diversity of biological processes such as cell proliferation and growth, cell fate determination, differentiation, and stem cell maintenance (Artavanis-Tsakonas et al, 1999;Bray, 2006). Recently, the Notch pathway has been proposed to play a crucial role in shell formation and pigmentation in molluscs, including pearl oysters (Pinctada margaritifera and P. fucata martensii) (Jiao et al, 2019;Auffret al, 2020), the clam (Meretrix meretrix) (Yue et al, 2015), and the Pacific oyster (Feng et al, 2015). Here, we first detected that this pathway underwent significant selection in different Pacific oyster populations, and some core genes of the pathway, i.e., Notch1 (two in GLD, one in XST, and one in QD) and Notch2 (one in GLD and one in QD and XST), were involved.…”