Transcriptional profiling of pigmentation-regulated long non-coding RNAs in the mantle of Manila clam (Ruditapes philippinarum)

Abstract

Long non-coding RNAs (lncRNAs) play important roles in a variety of biological processes and have received extensive attention in recent years. However, the expression and roles of lncRNAs in the Manila clam (Ruditapes philippinarum) are still poorly understood. In this study, we identified lncRNAs in the mantle of clams with different shell colors (orange (O), zebra (Z), white (W), and white zebra (WZ)). Using poly(A)-independent and strand-specific RNA-seq, we obtained 183,818,4888 clean reads and 32,541 lncRNA transcripts. In total, 1988 lncRNAs were identified as differentially expressed lncRNAs in comparisons between six pairs of groups. Fourteen mRNAs and their target genes were found to be related to the shell color pathway of melanin and porphyrin metabolism. Protein kinase C, calmodulin, melanogenesis associated transcription factor, peroxidase-like protein, tyrosine decarboxylase, myeloperoxidase, putativetyrosinase-like protein tyr-3, dopamine beta-hydroxylase, 5-aminolevulinate synthase, tyrosine aminotransferase, uroporphyrinogen-III synthase, hephaestin, delta-aminolevulinic acid dehydratase and ferrochelatase and their corresponding 77 cis-acting lncRNAs are thought to play important roles in the melanin synthesis pathway and porphyrin metabolic pathway. This study identified the catalog of lncRNAs expressed in the mantle of Manila clam, and the results provide insights into understanding the molecular regulation of shell color and genetic breeding in R. philippinarum.