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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.


Validation of expression analysis of miRNAs using qRT-PCR.Purple bars indicate the expression in the LTM tissue, while dark red bars indicate the expression in the tissue of RPT.
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pone.0134899.g005: Validation of expression analysis of miRNAs using qRT-PCR.Purple bars indicate the expression in the LTM tissue, while dark red bars indicate the expression in the tissue of RPT.

Mentions: Nine miRNAs were selected to validate expression analysis by performing qRT-PCR analysis in the LTM and RPT tissues. These included miR-9-3p, miR-29b, miR-31, miR-124, miR-133, miR-200-3p, miR-210, miR-2006 and miR-2008. As shown in Fig 5, the results of qRT-PCR and small RNA-Seq expression analysis for the nine miRNAs in the LTM and RPT were compared, suggesting that high consistence was observed for majority of miRNAs except for miR-29b and miR-210 (Fig 5).


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)

Validation of expression analysis of miRNAs using qRT-PCR.Purple bars indicate the expression in the LTM tissue, while dark red bars indicate the expression in the tissue of RPT.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134899.g005: Validation of expression analysis of miRNAs using qRT-PCR.Purple bars indicate the expression in the LTM tissue, while dark red bars indicate the expression in the tissue of RPT.
Mentions: Nine miRNAs were selected to validate expression analysis by performing qRT-PCR analysis in the LTM and RPT tissues. These included miR-9-3p, miR-29b, miR-31, miR-124, miR-133, miR-200-3p, miR-210, miR-2006 and miR-2008. As shown in Fig 5, the results of qRT-PCR and small RNA-Seq expression analysis for the nine miRNAs in the LTM and RPT were compared, suggesting that high consistence was observed for majority of miRNAs except for miR-29b and miR-210 (Fig 5).

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.