Characterization and expression analysis of microRNAs in the tube foot of sea cucumber Apostichopus japonicus.
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.
Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China.
Hongdi
H
Wang
The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, Alabama, United States of America.
Shikai
S
Liu
Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China.
Jun
J
Cui
Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China.
Chengze
C
Li
Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China.
Xuemei
X
Qiu
Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China.
Yaqing
Y
Chang
The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, Alabama, United States of America.
Zhanjiang
Z
Liu
Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China.
Xiuli
X
Wang
D000818:Animals; D001482:Base Composition; D019295:Computational Biology; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D009690:Nucleic Acid Conformation; D034622:RNA Interference; D015203:Reproducibility of Results; D012616:Sea Cucumbers / Q000235:genetics*; D059467:Transcriptome
D035683:MicroRNAs