Abstract
Shell-color polymorphism is a common phenomenon in several mollusk species and has been associated with thermal capacity, developmental stability, shell strength, and immunity. Shell-color polymorphism has been related to the differential expression of genes in several signal transduction pathways; however, the functions of micro-RNAs (miRNAs) in shell-color formation remain unclear. In the present study, we compared high-quality, small-RNA transcriptomes in three strains of the Manila clam Ruditapes philippinarum with specific shell-color patterns, artificially selected for six generations. Totals of 114 known and 208 novel miRNAs were identified by high-throughput sequencing, of which nine known and one novel miRNA were verified by stem-loop quantitative real time-polymerase chain reaction. Predicted miRNA targets were subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. miR-137 and miR-216b and the Hedgehog signaling pathway and Wnt signaling pathway were identified as being potentially involved in pigment formation and regulation in R. philippinarum. These results may help to clarify the role of miRNAs in shell coloration and shed light on the mechanisms regulating color formation in bivalve shells.
Highlights
Shell-color polymorphism is a common phenomenon among mollusks
These results suggest that miRNAs may play a role in the formation of shell color; no miRNAs have yet been demonstrated to be involved in the determination of mollusk shell color
There were 10 significantly differentially expressed miRNAs (DEMs) in Wh compared with Or, 104 significant DEMs in Wh compared with zebra stripe (Zs) (51 upregulated and 53 downregulated), and 52 significant DEMs in Or compared with Zs (22 upregulated and 30 downregulated) (Fig. 2; Supplementary Table S3)
Summary
Shell-color polymorphism is a common phenomenon among mollusks. Shell pigmentation has been potentially associated with various factors, including p redation[1], climatic effects[2,3], thermal c apacity[2,4,5], developmental stability[6], shell strength[7], and immunity[8,9]. The miRNAs pm-miR-2386 and pm-miR-13b were predicted to participate in biomineralization in the pearl oyster Pinctada martensii by regulating the formation of the organic matrix or the differentiation of mineralogenic cells during shell formation[30], while miR-2305 was shown to participate in nacre formation in the shell[31]. These results suggest that miRNAs may play a role in the formation of shell color; no miRNAs have yet been demonstrated to be involved in the determination of mollusk shell color. We constructed high-quality small-RNA transcriptomes for three shell-color lines of the Manila clam Ruditapes philippinarum, to provide basic data to further our understanding of the mechanisms regulating shell-color formation in this species
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