Identification and Characterization of miRNAs in Chondrus crispus by High-Throughput Sequencing and Bioinformatics Analysis.

Fan Gao,Wei Song,Fangru Nan,Jia Feng,Junping Lv,Shulian Xie

doi:10.1038/srep26397

Abstract

Chondrus crispus, an economically and medicinally important red alga, is a medicinally active substance and important for anti-tumor research. In this study, 117 C. crispus miRNAs (108 conserved and 9 novel) were identified from 2,416,181 small-RNA reads using high-throughput sequencing and bioinformatics methods. According to the BLAST search against the miRBase database, these miRNAs belonged to 110 miRNA families. Sequence alignment combined with homology searching revealed both the conservation and diversity of predicted potential miRNA families in different plant species. Four and 19 randomly selected miRNAs were validated by northern blotting and stem-loop quantitative real-time reverse transcription polymerase chain reaction detection, respectively. The validation rates (75% and 94.7%) demonstrated that most of the identified miRNAs could be credible. A total of 160 potential target genes were predicted and functionally annotated by Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes analysis. We also analyzed the interrelationship of miRNAs, miRNA-target genes and target genes in C. crispus by constructing a Cytoscape network. The 117 miRNAs identified in our study should supply large quantities of information that will be important for red algae small RNA research.

Highlights

The discovery of small RNAs that regulate diverse biological functions represents one of the most important findings in modern biology[1]
A small-RNA population isolated from total RNA of C. crispus was subjected to high-throughput sequencing (HiSeq)
According to the simulated chromosomes distribution of small RNAs illustrated in Fig. 1B, most small RNAs were distributed on either strand at contig435–contig[870], with the highest number of small RNAs distributed on the antisense strand around contig[705]

Summary

Introduction

The discovery of small RNAs that regulate diverse biological functions represents one of the most important findings in modern biology[1]. After the formation of a complex via loading of miRNAs into the RISC, mRNA degradation or translational inhibition is controlled by binding between the miRNA-RISC complex and complementary target mRNA8 Since their initial discovery as regulators in Caenorhabditis elegans, many miRNAs have been identified and demonstrated they play crucial roles in various plant and animal biological processes[9]. Extracted from C. crispus growing along the southern coast of Ireland in 18th century This substance has been recently used as a food additive as well as the main source of algal polysaccharide, which has valuable medicinal and health-related properties, such as tumor and virus inhibition, hypertension and hyperlipemia prevention, control of hyperglycemia, immunity enhancement, and antioxidant, antibacterial and anti-inflammatory activities[30,31,32,33,34,35,36,37,38,39,40,41]. Identification and characterization of miRNAs in C. crispus will be the essential first step in these tasks

Methods

Results

Conclusion