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

Wang H, Liu S, Cui J, Li C, Hu Y, Zhou W, Chang Y, Qiu X, Liu Z, Wang X - PLoS ONE (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China.

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.

No MeSH data available.


GO analysis for predicted target genes of differentially expressed miRNAs.The dark red bars indicate the gene numbers/percentages within each GO term at level 2 in the LTM, and the grey bars indicated the gene numbers/percentages within each GO term at level 2 in the RPT.
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pone.0134899.g006: GO analysis for predicted target genes of differentially expressed miRNAs.The dark red bars indicate the gene numbers/percentages within each GO term at level 2 in the LTM, and the grey bars indicated the gene numbers/percentages within each GO term at level 2 in the RPT.

Mentions: The target gene prediction for differentially expressed miRNAs with foldchange values >10 or <-10 revealed that 985 and 1,289 genes were predicted in LTM and RPT, respectively. The sequences of these target genes were listed in S3 and S4 Files. GO analysis showed that these genes were involved in numerous processes at GO level 2 (Fig 6). No significant difference in GO terms were observed between LTM and RPT. KEGG analysis indicated that a total of 37 and 44 KEGG pathways were only found in LTM or RPT, respectively. A total of 162 KEGG pathways were shared by LTM and RPT (Fig 7). The details information of KEGG pathways were provided in S3 Table.


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

Wang H, Liu S, Cui J, Li C, Hu Y, Zhou W, Chang Y, Qiu X, Liu Z, Wang X - PLoS ONE (2015)

GO analysis for predicted target genes of differentially expressed miRNAs.The dark red bars indicate the gene numbers/percentages within each GO term at level 2 in the LTM, and the grey bars indicated the gene numbers/percentages within each GO term at level 2 in the RPT.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4526669&req=5

pone.0134899.g006: GO analysis for predicted target genes of differentially expressed miRNAs.The dark red bars indicate the gene numbers/percentages within each GO term at level 2 in the LTM, and the grey bars indicated the gene numbers/percentages within each GO term at level 2 in the RPT.
Mentions: The target gene prediction for differentially expressed miRNAs with foldchange values >10 or <-10 revealed that 985 and 1,289 genes were predicted in LTM and RPT, respectively. The sequences of these target genes were listed in S3 and S4 Files. GO analysis showed that these genes were involved in numerous processes at GO level 2 (Fig 6). No significant difference in GO terms were observed between LTM and RPT. KEGG analysis indicated that a total of 37 and 44 KEGG pathways were only found in LTM or RPT, respectively. A total of 162 KEGG pathways were shared by LTM and RPT (Fig 7). The details information of KEGG pathways were provided in S3 Table.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China.

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.

No MeSH data available.