title: Identification and Characterization of MicroRNAs from Longitudinal Muscle and Respiratory Tree in Sea Cucumber (Apostichopus japonicus) Using High-Throughput Sequencing.
abstract: MicroRNAs (miRNAs), as a family of non-coding small RNAs, play important roles in the post-transcriptional regulation of gene expression. Sea cucumber (Apostichopus japonicus) is an important economic species which is widely cultured in East Asia. The longitudinal muscle (LTM) and respiratory tree (RPT) are two important tissues in sea cucumber, playing important roles such as respiration and movement. In this study, we identified and characterized miRNAs in the LTM and RPT of sea cucumber (Apostichopus japonicus) using Illumina HiSeq 2000 platform. A total of 314 and 221 conserved miRNAs were identified in LTM and RPT, respectively. In addition, 27 and 34 novel miRNAs were identified in the LTM and RPT, respectively. A set of 58 miRNAs were identified to be differentially expressed between LTM and RPT. Among them, 9 miRNAs (miR-31a-3p, miR-738, miR-1692, let-7a, miR-72a, miR-100b-5p, miR-31b-5p, miR-429-3p, and miR-2008) in RPT and 7 miRNAs (miR-127, miR-340, miR-381, miR-3543, miR-434-5p, miR-136-3p, and miR-300-3p) in LTM were differentially expressed with foldchange value being greater than 10. A total of 14,207 and 12,174 target genes of these miRNAs were predicted, respectively. Functional analysis of these target genes of miRNAs were performed by GO analysis and pathway analysis. This result provided in this work will be useful for understanding biological characteristics of the LTM and RPT of sea cucumber and assisting molecular breeding of sea cucumber for aquaculture.
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China.
authors.forename: Hongdi
authors.initials: H
authors.lastname: Wang
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, United States of America.
authors.forename: Shikai
authors.initials: S
authors.lastname: Liu
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Cui
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China.
authors.forename: Chengze
authors.initials: C
authors.lastname: Li
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China; School of Science, Dalian Ocean University, Dalian 116023, China.
authors.forename: Yucai
authors.initials: Y
authors.lastname: Hu
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhou
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China.
authors.forename: Yaqing
authors.initials: Y
authors.lastname: Chang
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China.
authors.forename: Xuemei
authors.initials: X
authors.lastname: Qiu
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, United States of America.
authors.forename: Zhanjiang
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China.
authors.forename: Xiuli
authors.initials: X
authors.lastname: Wang
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling; D063990:Gene Ontology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D035683:MicroRNAs / Q000378:metabolism*; D009132:Muscles / Q000378:metabolism*; D012137:Respiratory System / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015398:Signal Transduction / Q000235:genetics; D047528:Stichopus / Q000235:genetics*
chemical_list: D035683:MicroRNAs