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

Type Article
Date 2020-09
Language English
Author(s) Auffret Pauline1, Le Luyer JeremyORCID1, Sham Koua Manaarii1, Quillien Virgile1, 2, Ky Chin-Long1, 3
Affiliation(s) 1 : Ifremer, UMR EIO 241, Centre du Pacifique, BP 49, 98719, Taravao, Tahiti, Polynéise française, France
2 : Ifremer, UMR LEMAR UBO CNRS Ifremer IRD 6539, ZI Pointe Diable CS 10070, F-29280, Plouzane, France
3 : IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, F-34090, Montpellier, France
Source Bmc Genomics (1471-2164) (Springer Science and Business Media LLC), 2020-09 , Vol. 21 , N. 1 , P. 662 (13p.)
DOI 10.1186/s12864-020-07015-w
Keyword(s) Pinctada margaritifera, Albinism, Pigmentation, RNA-seq, Notch signaling pathway, Tyrosinase, Biomineralization
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.

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Publisher's official version 13 1 MB Open access
Additional file 1. Lists of DEGs between the P. margaritifera albino phenotype and black wild-type phenotype, associated statistics and annotation for the three datasets (Juvenile, Mantle and Pearl.. 375 KB Open access
Additional file 2. Lists of common DEGs between the P. margaritifera albino phenotype and black wild-type phenotype overlapping the three datasets (Juvenile, Mantle and Pearl Sac). 44 KB Open access
Additional file 3. Lists of enriched GO terms in the P. margaritifera albino phenotype compared with the black wild-type phenotype in the three datasets (Juvenile, Mantle and Pearl Sac). 238 KB Open access
Additional file 4: (.docx) Fig. S1. Summarised REVIGO treemaps plot for gene ontology enrichment analysis between the P. margaritifera albino versus black wild-type phenotypes. Fig. S2. Signalling... 630 KB Open access
Additional file 5. List of tyrosinase-related transcripts in P. margaritifera reference transcriptome. 8 KB Open access
Additional file 6. List of 159 candidate SNPs, i.e., common SNPs among outliers detected with PCAdapt and phenotype-associated SNPs detected with lfmm, based on filtered SNPs called with Freebayes... 139 KB Open access
Additional file 7. List of transcripts showing significant differential splicing (adjusted p value < 0.01) in Juvenile and Mantle datasets. 178 KB Open access
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How to cite 

Auffret Pauline, Le Luyer Jeremy, Sham Koua Manaarii, Quillien Virgile, Ky Chin-Long (2020). Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest stages using multiple whole transcriptome sequencing. Bmc Genomics, 21(1), 662 (13p.). Publisher's official version : https://doi.org/10.1186/s12864-020-07015-w , Open Access version : https://archimer.ifremer.fr/doc/00652/76420/