Characterization and Expression Analysis of MicroRNAs in the Tube Foot of Sea Cucumber Apostichopus japonicus

Abstract

MicroRNAs (miRNAs) are a class of endogenous non-coding small RNA with average length of 22 nucleotides, participating in the post-transcriptional regulation of gene expression. In this study, we report the identification and characterization of miRNAs in the tube foot of sea cucumber (Apostichopus japonicus) by next generation sequencing with Illumina HiSeq 2000 platform. Through the bioinformatic analysis, we identified 260 conserved miRNAs and six novel miRNAs from the tube foot small RNA transcriptome. Quantitative realtime PCR (qRT-PCR) was performed to characterize the specific expression in the tube foot. The results indicated that four miRNAs, including miR-29a, miR-29b, miR-2005 and miR-278-3p, were significantly up-regulated in the tube foot. The target genes of the four specifically expressed miRNAs were predicted in silico and validated by performing qRT-PCR. Gene ontology (GO) and KEGG pathway analyses with the target genes of these four miRNAs were conducted to further understand the regulatory function in the tube foot. This is the first study to profile the miRNA transcriptome of the tube foot in sea cucumber. This work will provide valuable genomic resources to understand the mechanisms of gene regulation in the tube foot, and will be useful to assist the molecular breeding in sea cucumber.

Identification and Characterization of MicroRNAs from Longitudinal Muscle and Respiratory Tree in Sea Cucumber (Apostichopus japonicus) Using High-Throughput Sequencing

“…The most abundant miRNAs were miR-1c, miR-10, and miR-71c-5p in the LTM, while the most abundant miRNAs were miR-1c, miR-10, and miR-200-3p in the RPT. This observation was consistent with previous studies [ 9 , 10 , 12 ], in which miR-1c and miR-10 were reported to be highly expressed. Taken together, it’s clear that miR-1c and miR-10 were the top two abundant miRNAs in the various tissues of sea cucumber examined to date.…”

“…The small RNA length distribution showed that 20-24nt was the main length in both the LTM and RPT, which is the typical size range of miRNAs. This is consistent with other miRNA studies in echinoderm animals [ 12 , 28 – 30 ]. A total of 221 and 314 conserved miRNAs were identified from the RPT and LTM, of which 161 miRNAs were identified from both RPT and LTM, while 153 and 60 miRNAs were only identified from LTM and RPT, respectively.…”

“…Over 11 million short expressed reads were generated for the two tissues, respectively. Comparing to the data generated in previous studies [ 10 – 12 ], similar throughput of datasets were generated in this work, providing sufficient high quality data for data analysis. A total of 91,978 unique reads and 221,845 unique were identified from LTM and RPT, respectively.…”

“…Small RNA sequencing and data analysis was as described in the previous study [ 12 ]. Two small RNA sequencing libraries (one per each tissue) were constructed and sequenced using the Illumina HiSeq 2000 platform.…”

“…Another studies reported the high-throughput miRNA sequencing of respiratory tree tissue in normal and aestivation sea cucumbers, and revealed that four miRNAs were significantly over-expressed during aestivation in the respiratory tree [ 11 ]. A recent study by our group and collaborators reported the identification of significantly up-regulated expression of miRNAs in tube foot of sea cucumber using high-throughput sequencing [ 12 ].…”