ANALYSIS OF COMPLETE MITOCHONDRIAL GENOME SEQUENCES OF <i>GADUS MACROCEPHALUS</i>

MAO Ming-Guang; GU Jie; LIU Rui-Ting; CHEN Yu; WU Ling-Mei; JIANG Zhi-Qiang; JIANG Jie-Lan

doi:10.7541/2019.003

Volume 43 Issue 1

Dec. 2018

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ACTA HYDROBIOLOGICA SINICA > 2019 > 43(1): 17-26. > DOI: 10.7541/2019.003

MAO Ming-Guang, GU Jie, LIU Rui-Ting, CHEN Yu, WU Ling-Mei, JIANG Zhi-Qiang, JIANG Jie-Lan. ANALYSIS OF COMPLETE MITOCHONDRIAL GENOME SEQUENCES OF GADUS MACROCEPHALUS[J]. ACTA HYDROBIOLOGICA SINICA, 2019, 43(1): 17-26. DOI: 10.7541/2019.003

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ANALYSIS OF COMPLETE MITOCHONDRIAL GENOME SEQUENCES OF GADUS MACROCEPHALUS

1.
Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China
2.
Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China

Funds: Supported by the Foundation of Liaoning Provincial Education Department (LR2016009, QL201702); China Postdoctoral Science Foundation (2016M602391); Central Public-interest Scientific Institution Basal Research & Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, China, CAFS (2017HY-XKQ01-08]

Received Date: March 22, 2018
Rev Recd Date: May 15, 2018
Available Online: October 11, 2018
Published Date: December 31, 2018

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Abstract

Abstract

The next-generation sequencing technology was used to obtain the whole mitochondrial genome sequences of Gadus macrocephalus. The mitochondrial gene was annotated and its structure was analyzed. The results showed that the circular genome was 16569 bp in length with typical mtDNA components. The mitochondrial genome encodes 13 proteins and 22 tRNAs, 2 rRNAs and a D-Loop region. The base composition showed a tendency of high AT and AT weak negative skewness. There were five kinds of termination codon in the protein coding gene of G. macrocephalus mitochondria, including AGG and AGA which were commonly found in mammalian mitochondria. It was shown that most of the tRNA structures share the classical clover shape, but the tRNA-Ser^(GCT) is unique because of a shortage of DHU. Two sequences with the functions of TAS and CSB, as well as 17 bp pyrimidine-rich sequences were found in D-Loop region. The non-coding region contains a conserved sequence controlling the initiation of light chain replication (O_L) and a gene spacer with 74 bp. Based on the whole mitochondrial genome sequence and the Cytb gene, the phylogenetic trees were constructed separately with several cod fish that belong to Gadiformes. The results provide an important evidence to reveal the evolutionary status of the pacific cod.
- Gadus macrocephalus,
- Mitochondria,
- Genome,
- Phylogenetic evolution,
- AT skew

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[1]	孟庆闻, 苏锦祥, 缪学祖. 当代科技重要著作•农业领域, 鱼类分类学. 北京: 中国农业出版社. 1995, 532—533 Meng Q W, Su J X, Miao X Z. Contemporary Science and Technology Important Works Agricultural Field, Fish Taxonomy [M]. Beijing: China Agricultural Press. 1995, 532—533
[2]	高天翔, 张肖荣, 王丹, 等. 几种鳕鱼的生物学初步研究. 海洋湖沼通报, 2003, (1): 35—42 doi: 10.3969/j.issn.1003-6482.2003.01.006 Gao T X, Zhang X R, Wang D, et al. Preliminary biological studies on several gadidae fishes [J]. Transactions of Oceanology and Limnology, 2003, (1): 35—42 doi: 10.3969/j.issn.1003-6482.2003.01.006
[3]	陈京美, 刘小芳, 冷凯良, 等. 太平洋真鳕鱼卵营养成分分析与评价. 青岛大学学报(自然科学版), 2016, 29(2): 57—62 Chen J M, Liu X F, Leng K L, et al. Analysis and evaluation of nutritional components of Gadus macrocephalus roe [J]. Journal of Qingdao University(Natural Science Edition), 2016, 29(2): 57—62
[4]	Pauly D, Zeller D. Comments on FAOs State of World Fisheries and Aquaculture, (SOFIA 2016) [J]. Marine Policy, 2017, 77: 176—181 doi: 10.1016/j.marpol.2017.01.006
[5]	田维雅. 欧洲: 将减少鳕鱼捕捞配额. 农产品市场周刊, 2006, (47): 15 Tian W Y. Europe: Cod fishing quotas will be cut [J]. Agricultural Products Market Weekly, 2006, (47): 15
[6]	Mao M G, Jiang J L, Jiang Z Q, et al. Molecular characterization of caspase members and expression response to Nervous Necrosis Virus outbreak in Pacific cod [J]. Fish & Shellfish Immunology, 2018, 74: 559—566
[7]	Sun H, Jiang Z, Mao M, et al. Cloning and expression analysis of interferon regulatory factor 7 in the Pacific cod, Gadus microcephalus [J]. Fish & Shellfish Immunology, 2016, 49: 7—15
[8]	Xing L, Wen S, Mao M, et al. RAG1 and IgM detection in Pacific cod (Gadus microcephalus) using real-time PCR [J]. Journal of Fisheries of China, 2015, 39(4): 475—484
[9]	姜志强, 王伟, 王华, 等. 太平洋鳕人工孵化方法, CN103168730A. 2013 Jiang Z Q, Wang W, Wang H, et al. Pacific cod artificial hatching method, CN103168730A [P]. 2013
[10]	Mao M G, Li X, Perálvarez-Marín A, et al. Transcriptomic analysis and biomarkers (Rag1, and Igμ) for probing the immune system development in Pacific cod, Gadus macrocephalus [J]. Fish & Shellfish Immunology, 2015, 44(2): 622—632
[11]	尹伟力, 方绍庆, 耿金培, 等. 鳕鱼物种特异性鉴定的PCR方法研究. 动物医学进展, 2011, 32(2): 19—24 doi: 10.3969/j.issn.1007-5038.2011.02.005 Yin W L, Fang S Q, Geng J P, et al. Study on PCR method specific for ling species identification [J]. Progress in Veterinary Medicine, 2011, 32(2): 19—24 doi: 10.3969/j.issn.1007-5038.2011.02.005
[12]	Grant W S, Zhang C I, Kobayashi T, et al. Lack of genetic stock discretion in pacific cod (Gadus macrocephalus) [J]. Canadian Journal of Fisheries & Aquatic Sciences, 1987, 44(3): 490—498
[13]	李建华, 王继文. 动物线粒体DNA在进化遗传学研究中的应用. 生物学通报, 2005, 40(2): 5—7 doi: 10.3969/j.issn.0006-3193.2005.02.002 Li J H, Wang J W. Application of animal mitochondrial DNA in evolutionary genetics [J]. Bulletin of Biology, 2005, 40(2): 5—7 doi: 10.3969/j.issn.0006-3193.2005.02.002
[14]	Bernt M, Donath A, Jühling F, et al. MITOS: improved de novo metazoan mitochondrial genome annotation [J]. Molecular Phylogenetics & Evolution, 2013, 69(2): 313
[15]	李昂, 高天翔, 孙典荣. 中国近海与日本近海白姑鱼线粒体细胞色素b基因全序列比较分析. 中国水产科学, 2010, 17(6): 1166—1172 Li A, Gao T X, Sun D R. Comparative analysis of white croaker (Pennahia argentata) based on complete cytochrome b gene sequence in mitochondrial DNA [J]. Journal of Fishery Sciences of China, 2010, 17(6): 1166—1172
[16]	连总强, 滚双宝, 李力, 等. 基于第二代测序技术兰州鲇线粒体基因组全序列测定与分析. 水生生物学报, 2017, 41(2): 334—345 Lian Z Q, Gun S B, Li L, et al. Sequencing and Analysis of the complete mitochondrial genome of Silurus lanzhouensis based on next generation sequencing technologies [J]. Acta Hydrobiologica Sinica, 2017, 41(2): 334—345
[17]	Fischer C, Koblmüller S, Gülly C, et al. Complete mitochondrial DNA sequences of the threadfin cichlid (Petrochromis trewavasae) and the blunthead cichlid (Tropheus moorii) and patterns of mitochondrial genome evolution in cichlid fishes [J]. PLoS One, 2013, 8(6): 67048 doi: 10.1371/journal.pone.0067048
[18]	Shadel G S, Clayton D A. Mitochondrial DNA maintenance in vertebrates [J]. Annual Review of Biochemistry, 1997, 66(1): 409—435 doi: 10.1146/annurev.biochem.66.1.409
[19]	Hixson J E, Wong T W, Clayton D A. Both the conserved stem-loop and divergent 5′-flanking sequences are required for initiation at the human mitochondrial origin of light-strand DNA replication [J]. Journal of Biological Chemistry, 1986, 261(5): 2384
[20]	Zardoya R, Garrido-Pertierra A, Bautista J M. The complete nucleotide sequence of the mitochondrial DNA genome of the rainbow trout, Oncorhynchus mykiss [J]. Journal of Molecular Evolution, 1995, 41(6): 942—951
[21]	Mclean M J, Wolfe K H, Devine K M. Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes [J]. Journal of Molecular Evolution, 1998, 47(6): 691—696 doi: 10.1007/PL00006428
[22]	Weber C C, Hurst L D. Intronic AT skew is a defendable proxy for germline transcription but does not predict crossing-over or protein evolution rates in Drosophila melanogaster [J]. Journal of Molecular Evolution, 2010, 71(5—6): 415 doi: 10.1007/s00239-010-9395-2
[23]	Cheng Y, Wang R, Sun Y, et al. The complete mitochondrial genome of the small yellow croaker and partitioned Bayesian analysis of Sciaenidae fish phylogeny [J]. Genetics & Molecular Biology, 2012, 35(1): 191—199
[24]	郭新红, 刘少军, 刘巧, 等. 鱼类线粒体DNA研究新进展. 遗传学报, 2005, 31(9): 983—1000 Guo X H, Liu S J, Liu Q, et al. New progress on mitochondrial DNA in fish [J]. Journal of Genetics and Genomics, 2005, 31(9): 983—1000
[25]	Johansen S, Guddal P H, Johansen A T. Organization of the mitochondrial genome of Atlantic cod, Gadus morhua [J]. Nucleic Acids Research, 1990, 18(3): 411—419 doi: 10.1093/nar/18.3.411
[26]	毕潇潇, 高天翔, 肖永双, 等. 4种鳕鱼线粒体16S rRNA、COI和Cyt b基因片段序列的比较研究. 南方水产科学, 2009, 5(3): 46—52 doi: 10.3969/j.issn.1673-2227.2009.03.008 Bi X X, Gao T X, Xiao Y S, et al. Sequence comparison of mtDNA 16S rRNA, COⅠ and Cyt b gene fragments in four species of Gadidae fish [J]. Southern China Fisheries Science, 2009, 5(3): 46—52 doi: 10.3969/j.issn.1673-2227.2009.03.008

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