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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.


Common and specific unique reads obtained by deep sequencing of small RNA transcriptome in the longitudinal muscle (LTM) and respiratory tree (RPT).The pink denotes the specific unique reads from RPT, the green denotes the specific unique reads from LTM, and the purple denotes the common unique reads obtained from both LTM and RPT.
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pone.0134899.g001: Common and specific unique reads obtained by deep sequencing of small RNA transcriptome in the longitudinal muscle (LTM) and respiratory tree (RPT).The pink denotes the specific unique reads from RPT, the green denotes the specific unique reads from LTM, and the purple denotes the common unique reads obtained from both LTM and RPT.

Mentions: Deep sequencing of the two small RNA libraries yielded 11,207,408 and 11,032,104 raw reads for LTM and RPT, respectively. After trimming, 11,018,885 and 10,777,407 clean reads were obtained, including 91,978 and 221,845 unique reads for LTM and RPT, respectively (Table 1). The specific and common unique reads between LTM and RPT were identified as shown in Fig 1, which included 24,596 common reads generated from both LTM and RPT, while 67,382 and 197,249 unique reads were generated only from LTM and 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 unique reads obtained by deep sequencing of small RNA transcriptome in the longitudinal muscle (LTM) and respiratory tree (RPT).The pink denotes the specific unique reads from RPT, the green denotes the specific unique reads from LTM, and the purple denotes the common unique reads obtained from both LTM and RPT.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134899.g001: Common and specific unique reads obtained by deep sequencing of small RNA transcriptome in the longitudinal muscle (LTM) and respiratory tree (RPT).The pink denotes the specific unique reads from RPT, the green denotes the specific unique reads from LTM, and the purple denotes the common unique reads obtained from both LTM and RPT.
Mentions: Deep sequencing of the two small RNA libraries yielded 11,207,408 and 11,032,104 raw reads for LTM and RPT, respectively. After trimming, 11,018,885 and 10,777,407 clean reads were obtained, including 91,978 and 221,845 unique reads for LTM and RPT, respectively (Table 1). The specific and common unique reads between LTM and RPT were identified as shown in Fig 1, which included 24,596 common reads generated from both LTM and RPT, while 67,382 and 197,249 unique reads were generated only from LTM and 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.