Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest st
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RESEARCH ARTICLE
Open Access
Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest stages using multiple whole transcriptome sequencing Pauline Auffret1, Jérémy Le Luyer1, Manaarii Sham Koua1, Virgile Quillien1,2 and Chin-Long Ky1,3*
Abstract Background: Albino mutations are commonly observed in the animal kingdom, including in bivalves. In the blacklipped 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 phenotypeassociated 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. Keywords: Pinctada margaritifera, Albinism, Pigmentation, RNA-seq, Notch signaling pathway, Tyrosinase, Biomineralization * Correspondence: [email protected] 1 Ifremer, UMR EIO 241, Centre du Pacifique, BP 49, 98719 Taravao, Tahiti, Polynéise française, France 3 IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, F-34090 Montpellier, France Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative
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