Comparative Transcriptome Analysis of the Pacific Oyster Crassostrea gigas Characterized by Shell Colors: Identification of Genetic Bases Potentially Involved in Pigmentation

Abstract

Background: Shell color polymorphisms of Mollusca have contributed to development of evolutionary biology and population genetics, while the genetic bases and molecular mechanisms underlying shell pigmentation are poorly understood. The Pacific oyster (Crassostrea gigas) is one of the most important farmed oysters worldwide. Through successive family selection, four shell color variants (white, golden, black and partially pigmented) of C. gigas have been developed. To elucidate the genetic mechanisms of shell coloration in C. gigas and facilitate the selection of elite oyster lines with desired coloration patterns, differentially expressed genes (DEGs) were identified among the four shell color variants by RNA-seq.

Results: Digital gene expression generated over fifteen million reads per sample, producing expression data for 28,027 genes. A total number of 2,645 DEGs were identified from pair-wise comparisons, of which 432, 91, 43 and 39 genes specially were up-regulated in white, black, golden and partially pigmented shell of C. gigas, respectively. Three genes of Abca1, Abca3 and Abcb1 which belong to the ATP-binding cassette (ABC) transporters super-families were significantly associated with white shell formation. A tyrosinase transcript (CGI_10008737) represented consistent up-regulated pattern with golden coloration. We proposed that white shell variant of C. gigas could employ "endocytosis" to down-regulate notch level and to prevent shell pigmentation.

Conclusion: This study discovered some potential shell coloration genes and related molecular mechanisms by the RNA-seq, which would provide foundational information to further study on shell coloration and assist in selective breeding in C. gigas.

Fig 1. Oysters (Crassostrea gigas) represented four kinds of shell color variants.

WS, the oyster of whole white shell; BS, the oyster of whole black shell; GS, the oyster of whole golden shell; NS, the oyster of partially pigmentation shell.

Fig 2. Venn digrams and histograms for numbers comparisons of DEGs among four DGE libraries (W_ME, B_ME, G_ME, N_ME).

Venn digrams represented the shared or specific DEGs among three pair-wise comparison between some one DGE library with any one of the three. The numbers of the shared DEGs are in the cross area, while the numbers of the specific DGEs are in the single area. Histogram represented the numbers of down-regulated (red), up-regulated (blue), and annotation (yellow) genes of DEGs in every pair-wise comparison. (a), W_ME compared with other three libraries in pairs (b), B_ME compared with other three libraries in pairs (c), G_ME compared with other three libraries in pairs (d), N_ME compared with other three libraries in pairs.

Fig 3. Gene ontology classification of up-regulated genes in comparisons between WS with any of other three variants.

Orange represented molecular function, green represented biological process.

Fig 4. The endocytosis pathway was significantly enriched from the KEGG pathways and shared based on DEGs in comparisons of WS vs any of other three variants.

Genes with green background were discovered in the RNA-seq, and genes with red text were up-regulated in WS.