title: Comparative study the expression of calcium cycling genes in Bombay duck (Harpadon nehereus) and beltfish (Trichiurus lepturus) with different swimming activities.
abstract: 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.
authors.affiliation: Key Laboratory of Marine Ecology and Environment Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Department of Bioscience Technology, Chung Yuan Christian University, 32023 Chung-Li, Taiwan.
authors.forename: Gilbert
authors.initials: G
authors.lastname: Audira
authors.affiliation: Third Institute of Oceanography, SOA, Xiamen 361005, China; Open Research Fund Program of MATHAB, SOA, Shanghai 201206, China.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Li
authors.affiliation: Key Laboratory of Marine Ecology and Environment Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
authors.forename: Weiwei
authors.initials: W
authors.lastname: Xian
authors.affiliation: Department of Chemistry, Chung Yuan Christian University, 32023 Chung-Li, Taiwan.
authors.forename: Muhammed Muhsin
authors.initials: MM
authors.lastname: Varikkodan
authors.affiliation: Department of Bioscience Technology, Chung Yuan Christian University, 32023 Chung-Li, Taiwan; Center for Biomedical Technology, Chung Yuan Christian University, Chung-Li 32023, Taiwan; Center for Nanotechnology, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
authors.forename: Chung-Der
authors.initials: CD
authors.lastname: Hsiao
keywords: Beltfish; Bombay duck; Calcium cycling gene; Muscle; Transcriptome