The identification of microRNAs in the whitespotted bamboo shark (Chiloscyllium plagiosum) liver by Illumina sequencing

Abstract

MicroRNAs are indispensable players in the regulation of a broad range of biological processes. Here, we report the first deep sequencing of the whitespotted bamboo shark (Chiloscyllium plagiosum) liver. We mapped 91 miRNAs in the Callorhinchus milii genome that have previously been described in the Danio rerio, Fugu rubripes, Oryzias latipes, Xenopus laevis, Xenopus tropicalis, Homo sapiens, and Mus musculus. In addition, 156 new putative candidate (PC) C. plagiosum miRNAs were identified. From these 247 miRNAs, 39 miRNA clusters were identified, and the expression of these clustered miRNAs was observed to vary significantly. A total of 7 candidate miRNAs were selected for expression confirmation by stem-loop RT-PCR. This study resulted in the addition of a significant number of novel miRNA sequences to GenBank and laid the foundation for further understanding of the function of miRNAs in the regulation of C. plagiosum liver development.

Keywords: Bioinformatics; C. milii; C. plagiosum; Callorhinchus milii; Chiloscyllium plagiosum; Chiloscyllium plagiosum liver; Danio rerio; Deep sequencing; Dre; Fru; Fugu rubripes; Homo sapiens; Hsa; Mmu; Mus musculus; Ola; Oryzias latipes; PC miRNAs; Stem-loop RT-PCR; Xenopus laevis; Xenopus tropicalis; Xla; Xtr; miRNAs; microRNAs; putative candidate miRNAs.