Full-Length Transcriptome Analysis Identifies Candidate Molecular Features Associated with Golden-Lip Coloration in Pinctada fucata martensii

Shell and pearl coloration is an economically important trait in Pinctada fucata martensii, with the golden-lip phenotype associated with commercially valuable golden nacre. In this study, full-length transcriptome sequencing was used to characterize transcript-abundance and transcript-structure patterns in pooled mantle samples from golden- and silver-lip oysters, with one pooled Iso-Seq library generated for each tissue/color condition from three individuals. Among the analyzed mantle samples, the largest transcript-profile differences between the color-line libraries were observed in mantle pallial tissue. The ferritin heavy-chain gene fth1-a showed moderately higher normalized transcript abundance in the Y_MP library than in W_MP but did not meet the predefined twofold screening threshold for library-level abundance differences. RT-qPCR analysis of additional independent individuals showed significantly higher fth1-a expression in golden-lip oysters. A custom anti-PmFTH1-A antibody was evaluated by Western blotting, and immunofluorescence analysis detected PmFTH1-A immunoreactivity within the decalcified shell organic matrix. Candidate alternative-splicing and alternative-polyadenylation events were identified in transcripts associated with carotenoid-related processes and biomineralization. COL1A1 showed higher transcript abundance in Y_MP, and RT-qPCR analysis of additional individuals showed significantly higher COL1A1 expression in the golden-lip group. Additional library-level differences involved transcripts associated with immune and stress-response processes. Overall, this exploratory study identifies candidate transcriptional and transcript-structural differences between the analyzed golden- and silver-lip samples and provides independent experimental support for higher fth1-a and COL1A1 expression in golden-lip oysters. These candidates require functional investigation and validation in independently replicated populations before any evaluation as molecular markers for selective breeding.