Complete sequence and gene organization of mitochondrial genome of Megalobrama terminalis from Qiantang River

doi:10.3969/j.issn.1004-1524.2020.09.08

›› 2020, Vol. 32 ›› Issue (9): 1591-1608.DOI: 10.3969/j.issn.1004-1524.2020.09.08

• Animal Science • Previous Articles Next Articles

Complete sequence and gene organization of mitochondrial genome of Megalobrama terminalis from Qiantang River

LIU Kai, FENG Xiaoyu, MA Hengjia, XIE Nan^*

Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China

Received:2020-03-02 Online:2020-09-25 Published:2020-10-10

Abstract

Abstract: To study the mitochondrial genomic structure of Megalobrama terminalis Richardson from Qiantang River and phylogenetic relationship of Cultrinae subfamily, the amplification by PCR, sequencing, and software splicing were used to obtain complete mitochondrial genome of M. terminalis from Qiantang River, whose GenBank accession number was MN725725. The full-length sequence of the mitochondrial genome of M. terminalis from Qiantang River was 16 621 bp, and its base composition was A (31.23%), G (16.17%), C (27.87%), and T (24.73%). There were 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes in the mitochondrial genome. Except for NAD6, tRNA-Gln, tRNA-Ala, tRNA-Asn, tRNA-Cys, tRNA-Tyr, tRNA-Ser^(UCN), tRNA-Glu, and tRNA-Pro, the other genes were encoded on the H chain. The A+T content of the mitochondrial genome and protein-coding genes in the mitochondria of M. terminalis from Qiangjiang River was 55.97% and 55.86%, respectively. The mitochondrial genome, and protein-coding genes in the mitochondria had obvious AT preference. There were two interspersed repeats in the mitochondrial gene, which were located at the front end of the terminal associated sequences region and the 3'end of the control region in the mitochondrial control region, respectively. Of the 22 tRNA genes, except tRNA-Ser^(AGY), they had a typical clover secondary structure. Based on the comparison of BLAST, the consistency of M. terminalis from Qiantang River and Heilongjiang River was 99.76%, while the consistency of M. terminalis from Pearl River was 99.87%. Phylogenetic tree was constructed based on complete mitochondrial genomes of 15 species of Cultrinae subfamily belonging to 7 genera. The genetic relationship between Megalobrama and Parabramis was closer than that of Culter, and Megalobrama was far away from Hemiculter, Hemiculterella, and Metzia.

Key words: Megalobrama terminalis, mitochondrial genome, sequence analysis, phylogenetic tree

CLC Number:

LIU Kai, FENG Xiaoyu, MA Hengjia, XIE Nan. Complete sequence and gene organization of mitochondrial genome of Megalobrama terminalis from Qiantang River[J]. , 2020, 32(9): 1591-1608.

References

[1] 周传江, 马爱喆, 汪曦, 等. 鱼类线粒体基因组研究进展[J]. 河南师范大学学报(自然科学版), 2019, 47(2):74-82.
ZHOU C J, MA A Z, WANG X, et al.Progress on fish mitochondrial genome[J]. Journal of Henan Normal University (Natural Science), 2019, 47(2):74-82.(in Chinese with English abstract)
[2] 成庆泰, 郑葆珊. 中国鱼类系统检索[M]. 北京: 科学出版社, 1987.
[3] 冯晓宇. 浙江省三角鲂研究进展及示范推广情况[J]. 科学养鱼, 2009(10):40-41.
FENG X Y. Research progress and promotion of Megalobrama terminalis in Zhejiang Province[J]. Scientific Fish Farming, 2009(10):40-41.(in Chinese)
[4] 赖瑞芳, 张秀杰, 李艳和, 等. 鲂属鱼类线粒体基因组的比较及其系统发育分析[J]. 水产学报, 2014, 38(1):1-14.
LAI R F, ZHANG X J, LI Y H, et al.Comparison of mitochondrial genomes of the genus Megalobrama and their phylogenetic analysis[J]. Journal of Fisheries of China, 2014, 38(1):1-14.(in Chinese with English abstract)
[5] HU X S, LUAN P X, CAO C H, et al.Characterization of the mitochondrial genome of Megalobrama terminalis in the Heilong River and a clearer phylogeny of the genus Megalobrama[J]. Scientific Reports, 2019, 9(1):8509.
[6] OKONECHNIKOV K, GOLOSOVA O, FURSOV M.Unipro UGENE: a unified bioinformatics toolkit[J]. Bioinformatics, 2012, 28(8):1166-1167.
[7] ALTSCHUL S F, MADDEN T L, SCHÄFFER A A, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs[J]. Nucleic Acids Research, 1997, 25(17):3389-3402.
[8] THE RNACENTRAL CONSORTIUM.RNAcentral: a hub of information for non-coding RNA sequences[J]. Nucleic Acids Research, 2019, 47(D1): D221-D229.
[9] LOWE T M, CHAN P P. tRNAscan-SE on-line: integrating search and context for analysis of transfer RNA genes[J]. Nucleic Acids Research, 2016, 44(W1):W54-W57.
[10] DARTY K, DENISE A, PONTY Y.VARNA: Interactive drawing and editing of the RNA secondary structure[J]. Bioinformatics (Oxford, England), 2009, 25(15):1974-1975.
[11] ZUKER M.Mfold web server for nucleic acid folding and hybridization prediction[J]. Nucleic Acids Research, 2003, 31(13):3406-3415.
[12] TARAILO-GRAOVAC M, CHEN N S. Using RepeatMasker to identify repetitive elements in genomic sequences[J]. Current Protocols in Bioinformatics, 2009, 25(1):4.10.1-4.10.14.
[13] IWASAKI W, FUKUNAGA T, ISAGOZAWA R, et al.MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline[J]. Molecular Biology and Evolution, 2013, 30(11):2531-2540.
[14] GRANT J R, ARANTES A S, STOTHARD P.Comparing thousands of circular genomes using the CGView comparison tool[J]. BMC Genomics, 2012, 13(1):1-8.
[15] KUMAR S, STECHER G, LI M, et al.MEGA X: molecular evolutionary genetics analysis across computing platforms[J]. Molecular Biology and Evolution, 2018, 35(6):1547-1549.
[16] SHARP P M, LI W H.An evolutionary perspective on synonymous codon usage in unicellular organisms[J]. Journal of Molecular Evolution, 1986, 24(1/2):28-38.
[17] NGUYEN L, SCHMIDT H A, VON HAESELER A, et al.IQ-TREE: a fast and effective stochastic algorithm for estimating maximum likelihood phylogenies[J]. Molecular Biology and Evolution, 2015, 32(1):268-274.
[18] CANNONE J J, SUBRAMANIAN S, SCHNARE M N, et al.The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs[J]. BMC Bioinformatics, 2002, 3:2.
[19] Nomenclature Committee for the International Union of Biochemistry (NC-IUB). Nomenclature for incompletely specified bases in nucleic acid sequences[J]. European Journal of Biochemistry, 1985, 150(1): 1-5.
[20] JÜHLING F, MÖRL M, HARTMANN R K, et al. tRNAdb 2009: compilation of tRNA sequences and tRNA genes[J]. Nucleic Acids Research, 2009, 37(Database issue):D159-D162.
[21] SATOH T P, MIYA M, MABUCHI K, et al.Structure and variation of the mitochondrial genome of fishes[J]. BMC Genomics, 2016, 17(1):1-20.
[22] ROZOV A, DEMESHKINA N, KHUSAINOV I, et al.Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code[J]. Nature Communications, 2016, 7:10457.
[23] FERNÁNDEZ-SILVA P, ENRIQUEZ J A, MONTOYA J. Replication and transcription of mammalian mitochondrial DNA[J]. Experimental Physiology, 2003, 88(1):41-56.
[24] HYVÄRINEN A K, POHJOISMÄKI J L O, REYES A, et al. The mitochondrial transcription termination factor mTERF modulates replication pausing in human mitochondrial DNA[J]. Nucleic Acids Research, 2007, 35(19):6458-6474.
[25] SEUTIN G, LANG B F, MINDELL D P, et al.Evolution of the WANCY region in amniote mitochondrial DNA[J]. Molecular Biology and Evolution, 1994, 11(3):329-340.
[26] 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]. The Journal of Biological Chemistry, 1986, 261(5):2384-2390.
[27] BROUGHTON R E, MILAM J E, ROE B A.The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA[J]. Genome Research, 2001, 11(11):1958-1967.
[28] SBISÀ E, TANZARIELLO F, REYES A, et al.Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications[J]. Gene, 1997, 205(1/2):125-140.
[29] ZHANG W Z, XIONG X M, ZHANG X J, et al.Mitochondrial genome variation after hybridization and differences in the first and second generation hybrids of bream fishes[J]. PLoS One, 2016, 11(7):e0158915.
[30] 毛明光, 顾杰, 刘瑞婷, 等. 太平洋鳕线粒体全基因组测序及结构特征分析[J]. 水生生物学报, 2019, 43(1): 17-26.
MAO M G, GU J, LIU R T, et al.Analysis of complete mitochondrial genome sequences of Gadus macrocephalus[J]. Acta Hydrobiologica Sinica, 2019, 43(1): 17-26. (in Chinese with English abstract)
[31] LEE W J, CONROY J, HOWELL W H, et al.Structure and evolution of teleost mitochondrial control regions[J]. Journal of Molecular Evolution, 1995, 41(1):54-66.
[32] SACCONE C, PESOLE G, SBISÁ E.The main regulatory region of mammalian mitochondrial DNA: structure-function model and evolutionary pattern[J]. Journal of Molecular Evolution, 1991, 33(1):83-91.
[33] 朱世华, 郑文娟, 邹记兴, 等. 鲹科鱼类线粒体DNA控制区结构及系统发育关系[J]. 动物学研究, 2007, 28(6):606-614.
ZHU S H, ZHENG W J, ZOU J X, et al.Mitochondrial DNA control region structure and molecular phylogenetic relationship of Carangidae[J]. Zoological Research, 2007, 28(6):606-614.(in Chinese with English abstract)
[34] 史宝, 柳学周, 刘永山, 等. 黄条鰤线粒体全基因组测序及结构特征分析[J]. 中国水产科学, 2019, 26(3):405-415.
SHI B, LIU X Z, LIU Y S, et al.Complete sequence and gene organization of the mitochondrial genome of Seriola aureovittata[J]. Journal of Fishery Sciences of China, 2019, 26(3):405-415.(in Chinese with English abstract)
[35] 钟东, 赵贵军, 张振书, 等. 基因组内碱基分布整体均衡与局部不均衡的研究进展[J]. 遗传, 2002, 24(3):351-355.
ZHONG D, ZHAO G J, ZHANG Z S, et al.Advance in the entire balance and local unbalance of base distribution in genome[J]. Hereditas, 2002, 24(3):351-355.(in Chinese with English abstract)
[36] REUTER J S, MATHEWS D H.RNAstructure: software for RNA secondary structure prediction and analysis[J]. BMC Bioinformatics, 2010, 11:129.
[37] 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[J]. 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.(in Chinese with English abstract)
[38] WOLSTENHOLME D R, JEON K W. Mitochondrial genomes[M]. San Diego: Academic Press, 1992.
[39] 杨泽民, 谢数涛, 章群, 等. RNA二级结构预测及其在分子分类研究中的应用[J]. 安徽农业科学, 2012, 40(7):3919-3922,3944.
YANG Z M, XIE S T, ZHANG Q, et al.Prediction and application of RNA secondary structure in the study of molecular taxonomy[J]. Journal of Anhui Agricultural Sciences, 2012, 40(7):3919-3922,3944.(in Chinese with English abstract)
[40] 蔡珊珊, 徐胜勇, 宋娜, 等. 黄鲫线粒体DNA控制区结构及长度多态性分析[J]. 水生生物学报, 2014, 38(5):980-986.
CAI S S, XU S Y, SONG N, et al.Mitochondrial DNA control region structure and length polymorphism analysis of Setipinna tenuifilis[J]. Acta Hydrobiologica Sinica, 2014, 38(5):980-986.(in Chinese with English abstract)
[41] HAYASHI J, TAGASHIRA Y, YOSHIDA M C.Absence of extensive recombination between inter-and intraspecies mitochondrial DNA in mammalian cells[J]. Experimental Cell Research, 1985, 160(2):387-395.
[42] BROUGHTON R E, DOWLING T E.Evolutionary dynamics of tandem repeats in the mitochondrial DNA control region of the minnow Cyprinella spiloptera[J]. Molecular Biology and Evolution, 1997, 14(12):1187-1196.
[43] FABER J E, STEPIEN C A.Tandemly repeated sequences in the mitochondrial DNA control region and phylogeography of the pike-perches Stizostedion[J]. Molecular Phylogenetics and Evolution, 1998, 10(3):310-322.
[44] CLAYTON D A.Replication of animal mitochondrial DNA[J]. Cell, 1982, 28(4):693-705.
[45] 罗云林. 鲂属鱼类的分类整理[J]. 水生生物学报, 1990, 14(2):160-165.
LUO Y L.A revision of fishes of the cyprinid genus Megalobrama[J]. Acta Hydrobiologica Sinica, 1990, 14(2):160-165.(in Chinese with English abstract)
[46] 谢楠, 刘新轶, 冯晓宇, 等. 鲂属鱼类细胞色素b片段序列分析[J]. 现代农业科技, 2012(1):290-292.
XIE N, LIU X Y, FENG X Y, et al. Sequences analysis on mitochondrial cytochrome b gene fragment of Megalobrama spp[J]. Modern Agricultural Science and Technology, 2012(1):290-292.(in Chinese with English abstract)
[47] 陈杰, 李福贵, 黄创新, 等. 不同鳊鲂属鱼类群体的形态差异分析[J]. 上海海洋大学学报, 2014, 23(3):388-394.
CHEN J, LI F G, HUANG C X, et al.Morphological variations of genera Parabramis and Megalobrama teleost populations[J]. Journal of Shanghai Fisheries University, 2014, 23(3):388-394.(in Chinese with English abstract)
[48] 张倩倩, 陈杰, 蒋霞云, 等. 不同鳊鲂鱼类群体微卫星DNA指纹图谱的构建和遗传结构分析[J]. 水产学报, 2014, 38(1):15-22.
ZHANG Q Q, CHEN J, JIANG X Y, et al.Establishment of DNA fingerprinting and analysis on genetic structure of different Parabramis and Megalobrama populations with microsatellite[J]. Journal of Fisheries of China, 2014, 38(1):15-22.(in Chinese with English abstract)
[49] HOANG D T, CHERNOMOR O, VON HAESELER A, et al.UFBoot2: Improving the ultrafast bootstrap approximation[J]. Molecular Biology and Evolution, 2018, 35:518-522.

Complete sequence and gene organization of mitochondrial genome of Megalobrama terminalis from Qiantang River

RichHTML

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	NI Zheng, CHEN Liu, HUA Jionggang, YE Weicheng, YUN Tao, ZHU Yinchu, ZHANG Cun. Detection of leukaemia virus antigen and analysis of GP85 gene sequence in local chicken breeds in Zhejiang Province [J]. , 2020, 32(8): 1357-1362.
[2]	WANG Weike, SONG Jiling, LU Na, YUAN Weidong, YAN Jing, CHEN Guanping. Cloning and expression of the PpFBD1 involved in primordium formation of Pleurotus pulmonarius [J]. , 2020, 32(1): 93-97.
[3]	DEXI Cuomu, WANG Yin, YANG Zexiao, YAO Xueping, LUO Yan, LIAO Changyu, ZHANG Pengfei, JIANG Dike, XIANG Mingyuan, JIANG Ruijiao, SONG Yong. Epidemiological investigation of porcine epidemic diarrhea virus and sequence analysis of ORF3 and S1 genes in Sichuan from 2016 to 2018 [J]. , 2019, 31(9): 1423-1428.
[4]	YI Keke, YIN Wenqi, ZHOU Yuancheng, JIANG Jinzhen, ZHANG Baiyu, LI Zhongyin, YAN Qigui. Isolation and identification of 4 strains of porcine pseudorabies virus and analysis of main virulence genes [J]. , 2019, 31(9): 1429-1436.
[5]	LIU Jialin, LIU Shili, JIANG Wenping, CHENG Shun, CHI Meili, ZHENG Jianbo, JIA Yongyi, ZHAO Jinliang, YIN Shaowu, GU Zhimin. Cloning and bioinformatics analysis of GH gene and its flanking region in Odontobutis potamophila [J]. , 2019, 31(9): 1461-1470.
[6]	MA Jie, ZHENG Hao, ZHOU Ping, CHEN Chunyan, WU Rui, MA Wei, SONG Lei, SUN Bo. Cloning and sequence analysis of StBSKs gene of Solanum tuberosum [J]. , 2019, 31(8): 1224-1230.
[7]	WANG Yuanhong, LU Zhimin, ZHANG Xueqi, LIU Zimin, HU Zihui, YANG Kankan, LIU Hongmei, PAN Ling, PENG Kaisong, LI Yongdong, WANG Yong. Isolation, identification and phylogenetic analysis on gp85 gene of subgroup J avian leukosis virus [J]. , 2019, 31(5): 709-715.
[8]	BA Shaobo, SHI Lin, LI Qunjing, LIU Zhengkui, CHEN Lin, WANG Xiaodu, SONG Houhui. Isolation, identification and molecullar epidemiological analysis of 17-ZJ-HZ strain of porcine reproductive and respiratory syndrome virus [J]. , 2018, 30(8): 1303-1311.
[9]	LIU Shili, JIA Yongyi, JIANG Wenping, CHI Meili, CHENG Shun, ZHAO Jinliang, GU Zhimin, FU Jianjun. Cloning and sequence analysis of growth hormone gene and its flanking region in topmouth culter (Culter alburnus Basilewsky) [J]. , 2017, 29(8): 1281-1289.
[10]	YANG Hua, HE Xiangxiang, XIAO Yingping, QIAN Mingrong, ZHANG Qiaoyan, TANG Biao. Drug resistance spectrum analysis and MLST genotyping of Escherichia coli from refrigerated chicken in three regions of Zhejiang Province [J]. , 2017, 29(6): 888-893.
[11]	KONG Linglin, ZHENG Shenghan, CHEN Ying, ZHU Pengfei, WU Yun, GUO Qixin, CHEN Guohong, CHANG Guobin. Comparative analysis of DMA gene sequences in different chicken breeds [J]. , 2017, 29(4): 560-565.
[12]	WANG Yan, LIU Yao, LIANG Chenggang, CHEN Qingqing, SHI Taoxiong, CHEN Qijiao, MENG Ziye, CHEN Qingfu. Sequence analysis of ABA-insensitive gene of common buckwheat, Fagopyrum esculentum [J]. , 2017, 29(2): 186-192.
[13]	GAO Jianfeng, LU Zengkui, MA Youji, LI Taotao1, ZHAO Xingxu. Cloning, sequence analysis and tissue expression of MUSTN1 gene in sheep (Ovis aires) [J]. , 2017, 29(10): 1661-1668.
[14]	ZHANG Yang, WANG Meiqing, MU Chunyu, YAO Wencheng, YANG Yaozong, BIAN Youqing, CHEN Guohong. Analysis of mitochondrial CO Ⅰ gene bar code and its upstream tRNA sequence determination [J]. , 2017, 29(1): 51-57.
[15]	WU Yun， BI Yulin， ZHANG Yang， GUO Xiaomin， LI Zhiteng， WAN Fang， ZHU Pengfei， XU Lu， CHANG Guobin*， XU Qi， CHEN Guohong. SNP and Indel analysis of BG gene of some Chinese chicken breeds [J]. , 2016, 28(8): 1338-.