Identification of shell-color-related microRNAs in the Manila clam Ruditapes philippinarum using high-throughput sequencing of small RNA transcriptomes

• Published in: Scientific reports Vol. 11; no. 1; pp. 8044 - 8
• Main Authors: Ding, Jianfeng, Wen, Qiang, Huo, Zhongming, Nie, Hongtao, Qin, Yanjie, Yan, Xiwu
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 13.04.2021; Nature Publishing Group; Nature Portfolio
• Subjects: 631/181; 631/337; Animal Shells - metabolism; Animals; Bivalvia - genetics; Bivalvia - metabolism; Color; Coloration; Gene Expression Profiling; Gene polymorphism; Genomes; Hedgehog protein; High-Throughput Nucleotide Sequencing; Humanities and Social Sciences; MicroRNAs; MicroRNAs - genetics; MicroRNAs - metabolism; miRNA; Mollusks; multidisciplinary; Next-generation sequencing; Pigmentation - genetics; Polymerase chain reaction; Polymorphism; Ruditapes philippinarum; Science; Science (multidisciplinary); Signal transduction; Thermal capacity; Transcriptome; Wnt protein
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-021-86727-9

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.