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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.<\/jats:p>","DOI":"10.3390\/ani16192989","type":"journal-article","created":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T08:14:39Z","timestamp":1790151279000},"page":"2989","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Full-Length Transcriptome Analysis Identifies Candidate Molecular Features Associated with Golden-Lip Coloration in Pinctada fucata martensii"],"prefix":"10.3390","volume":"16","author":[{"given":"Yong","family":"Liu","sequence":"first","affiliation":[{"name":"Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"given":"Shuai","family":"Chen","sequence":"additional","affiliation":[{"name":"Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]},{"given":"Hongmei","family":"Yang","sequence":"additional","affiliation":[{"name":"Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"validation","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]},{"given":"Weilin","family":"Du","sequence":"additional","affiliation":[{"name":"Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Wenhao","family":"Yu","sequence":"additional","affiliation":[{"name":"Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Yuewen","family":"Deng","sequence":"additional","affiliation":[{"name":"Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China"},{"name":"Shenzhen Institute, Guangdong Ocean University, Shenzhen 518120, China"},{"name":"Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China"},{"name":"Pearl Research Institute, Guangdong Ocean University, Zhanjiang 524088, China"},{"name":"Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"resources","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0021-2524","authenticated-orcid":false,"given":"Zhe","family":"Zheng","sequence":"additional","affiliation":[{"name":"Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China"},{"name":"Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang 524088, China"},{"name":"Pearl Research Institute, Guangdong Ocean University, Zhanjiang 524088, China"},{"name":"Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"885","DOI":"10.1111\/j.1469-185X.2011.00177.x","article-title":"Colours of Domestication","volume":"86","author":"Cieslak","year":"2011","journal-title":"Biol. 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