Limits...
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.


Common and specific conserved miRNAs in the longitudinal muscle (LTM) and respiratory tree (RPT).The blue denotes the specific conserved miRNAs identified from LTM. The pink denotes specific conserved miRNAs identified in RPT, and the purple denotes the common conserved miRNAs in both LTM and RPT.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4526669&req=5

pone.0134899.g003: Common and specific conserved miRNAs in the longitudinal muscle (LTM) and respiratory tree (RPT).The blue denotes the specific conserved miRNAs identified from LTM. The pink denotes specific conserved miRNAs identified in RPT, and the purple denotes the common conserved miRNAs in both LTM and RPT.

Mentions: After removal of reads from other types of small RNAs identified as above, the remaining reads were used miRNA identification. A total of 221 conserved miRNAs were identified in LTM (S1 Table), and a total of 314 small RNAs were identified in RPT (S2 Table). As shown in Fig 3, a total of 161 conserved miRNAs were identified in both tissues, and 153 and 60 miRNAs were only found in LTM or RPT, respectively.


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)

Common and specific conserved miRNAs in the longitudinal muscle (LTM) and respiratory tree (RPT).The blue denotes the specific conserved miRNAs identified from LTM. The pink denotes specific conserved miRNAs identified in RPT, and the purple denotes the common conserved miRNAs in both LTM and RPT.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134899.g003: Common and specific conserved miRNAs in the longitudinal muscle (LTM) and respiratory tree (RPT).The blue denotes the specific conserved miRNAs identified from LTM. The pink denotes specific conserved miRNAs identified in RPT, and the purple denotes the common conserved miRNAs in both LTM and RPT.
Mentions: After removal of reads from other types of small RNAs identified as above, the remaining reads were used miRNA identification. A total of 221 conserved miRNAs were identified in LTM (S1 Table), and a total of 314 small RNAs were identified in RPT (S2 Table). As shown in Fig 3, a total of 161 conserved miRNAs were identified in both tissues, and 153 and 60 miRNAs were only found in LTM or RPT, respectively.

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.