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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.


Length distribution of small RNAs identified from the LTM (A) and RPT (B) of sea cucumber (A. japonicus).
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pone.0134899.g002: Length distribution of small RNAs identified from the LTM (A) and RPT (B) of sea cucumber (A. japonicus).

Mentions: The majority of identified small RNAs were with lengths of 20–23 nt for LTM, and 20–24 nt for RPT, as shown in Fig 2. Small RNAs with length of 22 nt were the most abundant (Fig 2). Based on the annotation with Rfam database, 7,619 small RNAs in the LTM were annotated, including rRNA (6,752), tRNA (733), snRNA (62) and snoRNA (72). Similarly, 28,657 small RNAs in the RPT were annotated, including rRNA (20939), tRNA (7131), snRNA (261) and snoRNA (326). The detailed information of identified small RNAs were provided in Table 2.


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)

Length distribution of small RNAs identified from the LTM (A) and RPT (B) of sea cucumber (A. japonicus).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134899.g002: Length distribution of small RNAs identified from the LTM (A) and RPT (B) of sea cucumber (A. japonicus).
Mentions: The majority of identified small RNAs were with lengths of 20–23 nt for LTM, and 20–24 nt for RPT, as shown in Fig 2. Small RNAs with length of 22 nt were the most abundant (Fig 2). Based on the annotation with Rfam database, 7,619 small RNAs in the LTM were annotated, including rRNA (6,752), tRNA (733), snRNA (62) and snoRNA (72). Similarly, 28,657 small RNAs in the RPT were annotated, including rRNA (20939), tRNA (7131), snRNA (261) and snoRNA (326). The detailed information of identified small RNAs were provided in Table 2.

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.