Genome‐wide association study analysis to resolve the key regulatory mechanism of biomineralization in Pinctada fucata martensii

Abstract

Biomineralization-controlled exo-/endoskeleton growth contributes to body growth and body size diversity. Molluscan shells undergo ectopic biomineralization to form the exoskeleton and biocalcified "pearl" involved in invading defence. Notably, exo-/ endoskeletons have a common ancestral origin, but their regulation and body growth are largely unknown. This study employed the pearl oyster, Pinctada fucata marntensii, a widely used experimental model for biomineralization in invertebrates, to perform whole-genome resequencing of 878 individuals from wild and breeding populations.This study characterized the genetic architecture of biomineralization-controlled growth and ectopic biomineralization. The insulin-like growth factor (IGF) endocrine signal interacted with ancient single-copy transcription factors to form the regulatory network. Moreover, the "cross-phylum" regulation of key long noncoding RNA (lncRNA) in bivalves and mammals indicated the conserved genetic and epigenetic regulation in exo-/endoskeleton growth. Thyroid hormone signal and apoptosis regulation in pearl oysters affected ectopic biomineralization in pearl oyster. These findings provide insights into the mechanism underlying the evolution and regulation of biomineralization in exo-/endoskeleton animals and ectopic biomineralization.

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

“…In the present study, genome-wide selection signals and genes were first identified in different Dalian populations. GO and KEGG enrichment analyses revealed biological processes related to DNA metabolism and stability, shell formation, and environmental stress response significantly enriched, and some similar selected processes have also been detected in other bivalves, such as the pearl oyster (Pinctada fucata martensii) (Zheng et al, 2023) and the bay scallop (Argopecten irradians) (Wang et al, 2021), which may be key processes in bivalves to adapt to environmental changes. A growing body of evidence proves that environmental stress can influence the genome stability of organisms (Galhardo et al, 2007).…”

“…The very thick shells in sessile oysters do provide a critical physical line for the species to defend against predation and desiccation (Zhang et al, 2012). Glycosaminoglycan, which has high calcium affinity, was suggested to play a key part in crystal nucleation in the process of the nacreous layer formation in shelled molluscs (Lopes-Lima et al, 2005;Du et al, 2017;Zheng et al, 2023). A study of selective sweep in different pearl oyster populations discovered that typical signaling pathways for biomineralization of shell formation, such as glycosaminoglycan biosynthesis, were under selection pressure (Zheng et al, 2023).…”

“…Glycosaminoglycan, which has high calcium affinity, was suggested to play a key part in crystal nucleation in the process of the nacreous layer formation in shelled molluscs (Lopes-Lima et al, 2005;Du et al, 2017;Zheng et al, 2023). A study of selective sweep in different pearl oyster populations discovered that typical signaling pathways for biomineralization of shell formation, such as glycosaminoglycan biosynthesis, were under selection pressure (Zheng et al, 2023). Consistent with the findings in the pearl oyster, pathways of glycosaminoglycan biosynthesis were also significantly enriched for the selected genes in the Pacific oyster populations in the present study.…”

“…With the advent of next-generation sequencing and the availability of genomes of many species, wholegenome sequencing has been a powerful tool for studying the population genetics of the species on a fine scale using genomewide single-nucleotide polymorphisms (SNPs). It also has the potential to identify genomic selection signatures and genes related to economic or adaptive important traits (Liu et al, 2017;Li et al, 2018;Wang et al, 2021;Li et al, 2022;Chen et al, 2023;Zheng et al, 2023).…”

Transcriptome analysis reveals core lncRNA-mRNA networks regulating melanization and biomineralization in Patinopecten yessoensis shell-infested by Polydora

“…With the prevalence of the next-generation sequencing, characterizations and expression patterns of lncRNAs in molluscs have been gradually investigated, and they are found functioning in diverse bioprocesses, covering immune and stress response [ 34 – 38 ], muscle growth [ 39 ], gametogenesis [ 40 ] and larval development [ 41 ]. Emerging evidence has also revealed that lncRNAs are involved in the modulation of shell biomineralization and pigmentation in molluscs [ 42 – 46 ]. For example, chorions peroxidase and its cis -acting lncRNA TCONS_00951105 were predicted to exhibit a key function in melanin biosynthesis in Pacific oysters ( Crassostrea gigas ) by RNA-seq [ 42 ]; in manila clam ( Ruditapes philippinarum ), 14 differential expressed mRNAs and their interactive 77 lncRNAs were thought to be involved in the pathways of melanin synthesis and porphyrin metabolic [ 45 ]; besides, a lncRNA named LncMSEN2 were identified functioning in exoskeleton formation in the pearl oyster ( Pinctada fucuta martensii ) [ 47 ].…”