Dataset Information

Identification of myogenic regulatory genes in the muscle transcriptome of beltfish (Trichiurus lepturus): A major commercial marine fish species with robust swimming ability.

ABSTRACT: The beltfish (Trichiurus lepturus) is considered as one of the most economically important marine fish in East Asia. It is a top predator with a robust swimming ability that is a good model to study muscle physiology in fish. In the present study, we used Illumina sequencing technology (NextSeq500) to sequence, assemble and annotate the muscle transcriptome of juvenile beltfish. A total of 57,509,280 clean reads (deposited in NCBI SRA database with accession number of SRX1674471) were obtained from RNA sequencing and 26,811 unigenes (with N50 of 1033 bp) were obtained after de novo assembling with Trinity software. BLASTX against NR, GO, KEGG and eggNOG databases show 100%, 49%, 31% and 96% annotation rate, respectively. By mining beltfish muscle transcriptome, several key genes which play essential role on regulating myogenesis, including pax3, pax7, myf5, myoD, mrf4/myf6, myogenin and myostatin were identified with a low expression level. The muscle transcriptome of beltfish can provide some insight into the understanding of genome-wide transcriptome profile of teleost muscle tissue and give useful information to study myogenesis in juvenile/adult fish.

SUBMITTER: Zhang H

PROVIDER: S-EPMC4856820 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

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Identification of myogenic regulatory genes in the muscle transcriptome of beltfish (Trichiurus lepturus): A major commercial marine fish species with robust swimming ability.

Zhang Hui H Chang Chung-Ming CM Shen Kang-Ning KN Xian Weiwei W Hsiao Chung-Der CD

Genomics data 20160417

The beltfish (Trichiurus lepturus) is considered as one of the most economically important marine fish in East Asia. It is a top predator with a robust swimming ability that is a good model to study muscle physiology in fish. In the present study, we used Illumina sequencing technology (NextSeq500) to sequence, assemble and annotate the muscle transcriptome of juvenile beltfish. A total of 57,509,280 clean reads (deposited in NCBI SRA database with accession number of SRX1674471) were obtained f ...[more]

PMID: 27222805

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Project description:The contraction and relaxation events of the muscle is mediated by the coordination of many important calcium cycling proteins of ryanodine receptor (RYR), troponin C (TNNC), parvalbumin (PVALB), sarcoendoplasmic reticulum calcium transport ATPase (SERCA) and calsequestrin (CASQ). In higher vertebrates, the expression level of calcium cycling proteins are positively correlated to the muscle contraction/relaxation ability of the cell. In this study, we used RNAseq to explore the expression profile of calcium cycling genes between two marine fish of Bombay duck (Harpadon nehereus) and beltfish (Trichiurus lepturus) with poor and robust swimming activities, respectively. We have studied the hypothesis whether the expression level of calcium cycling proteins are also positive correlated to swimming ability in fish. We used Illumina sequencing technology (NextSeq500) to sequence, assemble and annotate the muscle transcriptome of Bombay duck for the first time. A total of 47,752,240 cleaned reads (deposited in NCBI SRA database with accession number of SRX1706379) were obtained from RNA sequencing and 26,288 unigenes (with N50 of 486 bp) were obtained after de novo assembling with Trinity software. BLASTX against NR, GO, KEGG and eggNOG databases show 100%, 65%, 26%, 94% and 88% annotation rate, respectively. Comparison of the dominantly expressed unigenes in fish muscle shows calcium cycling gene expression in beltfish (SRX1674471) is 1.4- to 51.6-fold higher than Bombay duck. Among five calcium cycling genes, the fold change results are very significant in CASQ (51.6 fold) and PVALB (9.1 fold) and both of them are responsive for calcium binding to reduce free calcium concentration in the sarcoendoplasmic reticulum and cytoplasm. In conclusion, we confirmed that the high abundant expression rate of calcium cycling genes in robust swimming fish species. The current muscle transcriptome and identified calcium cycling gene data can provide more insights into the muscle physiology of fish.

Dataset Information

Identification of myogenic regulatory genes in the muscle transcriptome of beltfish (Trichiurus lepturus): A major commercial marine fish species with robust swimming ability.

Publications

Identification of myogenic regulatory genes in the muscle transcriptome of beltfish (Trichiurus lepturus): A major commercial marine fish species with robust swimming ability.

Similar Datasets

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