黄条鰤线粒体全基因组测序及结构特征分析
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摘要
通过二代测序、软件拼接获得中国黄海海域黄条鰤(Seriola aureovittata)线粒体基因组全序列。其序列全长为16609 bp,碱基组成分别为A(26.68%)、G(17.84%)、C(30.12%)和T(25.36%);共有13条蛋白编码基因, 22个tRNA基因, 2个rRNA基因,除NAD6、trnQ、trnA、trnN、trnC、trnY、trnS、trnE、trnP外,其余基因均在H链上编码。黄条鰤线粒体基因组全序列与蛋白编码基因的A+T含量分别为52.05%和51.085%,具有明显的AT偏好性。线粒体基因中存在2个散在重复序列,分别位于NAD1基因序列正义链的中游和COX2基因序列反义链的上游。在其22个tRNA基因中,除了tRNAGly外,均具有典型的三叶草二级结构。黄条鰤线粒体基因组的蛋白编码基因起止位点与密码子除COX1、NAD5外,均与日本海域出产的黄条鰤(Seriola lalandi)完全吻合,且COX1、NAD5基因皆短于日本黄条鰤;两者间存在一定的遗传差异。基于18种隶属于13属的鲹科鱼类线粒体基因组全序列构建系统发生树,可知小甘鲹(Seriolina nigrofasciata)、黄条鰤、五条鰤(Seriola quinqueradiata)、高体鰤(Seriola dumerili)、长鳍鰤(Seriola rivoliana)同属一近支,且黄条鰤与五条鰤亲缘关系最近,与小甘鲹进化距离较远。
Seriola aureovittata is a large marine pelagic predatory fish species in the global warm temperate ocean,which is mainly distributed near the offshore rocks and reefs of the Bohai Sea and Yellow Sea of China. In recent years, most research has focused on its breeding and breeding technology at home and abroad, whereas few studies have been conducted on its genome and group composition. The complete mitochondrial DNA was extracted from the somatic side muscles of S. aureovittata. The complete mitochondrial genome of S. aureovittata was obtained using second generation sequencing and splicing with software of DNAStar. The sequence length was 16609 bp,and the base composition was A(26.68%), G(17.84%), C(30.12%), and T(25.36%). It contained 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes. Except for NAD6, trnQ, trnA, trnN, trnC, trnY, trnS, trnE,and trnP, all the other genes were encoded on the heavy strand(H strand). The A+T content of the complete mitochondrial genome sequence and protein-coding genes were 52.05% and 51.085%, respectively. There was a strong bias toward A+T in the genome of S. aureovittata. There were two repeated sequences scattered in the genes.One was located in the middle part of the sense strand of the NAD1 gene sequence, and the other was located in the upper part of the antisense strand of COX2 gene sequence. All tRNA genes had typical cloverleaf structure except tRNAGly. Its start-stop sites and codons of protein-coding genes, except COX1 and NAD5, were the same as that of Seriola lalandi, which inhabits in the oceans of Japan. The COX1 and NAD5 protein genes of S. aureovittata were shorter than those of S. lalandi. It was preliminarily assumed that there were genetic differences between S.aureovittata and S. lalandi. The NJ-tree based on the complete mitochondrial DNA genomes showed the evolutionary position of S. aureovittata relative to that of 18 other Carangidae species. The results showed that the Seriola spp. belong to a secondary tree with Seriolina nigrofasciata. Furthermore, S. aureovittata and Seriolina quinqueradiata had a closer relationship than others in the tree, whereas S. aureovittata had the most distant relationship with S. nigrofasciata. This study provides basic data for solving different geographical population and kinship relations of S. aureovittata.
Seriola aureovittata is a large marine pelagic predatory fish species in the global warm temperate ocean,which is mainly distributed near the offshore rocks and reefs of the Bohai Sea and Yellow Sea of China. In recent years, most research has focused on its breeding and breeding technology at home and abroad, whereas few studies have been conducted on its genome and group composition. The complete mitochondrial DNA was extracted from the somatic side muscles of S. aureovittata. The complete mitochondrial genome of S. aureovittata was obtained using second generation sequencing and splicing with software of DNAStar. The sequence length was 16609 bp,and the base composition was A(26.68%), G(17.84%), C(30.12%), and T(25.36%). It contained 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes. Except for NAD6, trnQ, trnA, trnN, trnC, trnY, trnS, trnE,and trnP, all the other genes were encoded on the heavy strand(H strand). The A+T content of the complete mitochondrial genome sequence and protein-coding genes were 52.05% and 51.085%, respectively. There was a strong bias toward A+T in the genome of S. aureovittata. There were two repeated sequences scattered in the genes.One was located in the middle part of the sense strand of the NAD1 gene sequence, and the other was located in the upper part of the antisense strand of COX2 gene sequence. All tRNA genes had typical cloverleaf structure except tRNAGly. Its start-stop sites and codons of protein-coding genes, except COX1 and NAD5, were the same as that of Seriola lalandi, which inhabits in the oceans of Japan. The COX1 and NAD5 protein genes of S. aureovittata were shorter than those of S. lalandi. It was preliminarily assumed that there were genetic differences between S.aureovittata and S. lalandi. The NJ-tree based on the complete mitochondrial DNA genomes showed the evolutionary position of S. aureovittata relative to that of 18 other Carangidae species. The results showed that the Seriola spp. belong to a secondary tree with Seriolina nigrofasciata. Furthermore, S. aureovittata and Seriolina quinqueradiata had a closer relationship than others in the tree, whereas S. aureovittata had the most distant relationship with S. nigrofasciata. This study provides basic data for solving different geographical population and kinship relations of S. aureovittata.
引文
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[12]Martinez-Takeshita N,Purcell C M,Chabot C L,et al.A tale of three tails:Cryptic speciation in a globally distributed marine fish of the genus,Seriola[J].Copeia,2015,103(2):357-368.
[13]Shi B,Liu Y S,Liu X Z,et al.Study on the karyotype of yellowtail kingfish(Seriola aureovittata)[J].Progress in Fishery Sciences,2017,38(1):136-141.[史宝,刘永山,柳学周,等.黄条鰤(Seriola aureovittata)染色体核型分析[J].渔业科学进展,2017,38(1):136-141.]
[14]Meng Q W,Su J X,Miao X Z.Systematics of Fishes[M].Beijing:China Agriculture Press,1995:672-673.[孟庆闻,苏锦祥,缪学祖.鱼类分类学[M].北京:中国农业出版社,1995:672-673.]
[15]Balanov A A.On the species composition of fish of the genus Seriola(Carangidae)in the northwestern part of the Sea of Japan[J].Journal of Ichthyology,2008,48(6):415-421.
[16]Beaumont A.Genetics and evolution of aquatic organisms[J].Reviews in Fish Biology and Fisheries,1995,5(3):385-386.
[17]Burland T G.DNASTAR’s Lasergene sequence analysis software[M]//Bioinformatics Methods and Protocols.Totowa:Humana Press,2000,132:71-91.
[18]Thompson J D,Gibson T J,Plewniak F,et al.The CLUSTAL_X windows interface:flexible strategies for multiple sequence alignment aided by quality analysis tools[J].Nucleic Acids Research,1997,25(24):4876-4882.
[19]Kumar S,Stecher G,Peterson D,et al.MEGA-CC:computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis[J].Bioinformatics,2012,28(20):2685-2686.
[20]Xiao W H,Zhang Y P.Genetics and evolution of mitochondrial DNA in fish[J].Acta Hydrobiologica Sinica,2000,24(4):384-391.[肖武汉,张亚平.鱼类线粒体DNA的遗传与进化[J].水生生物学报,2000,24(4):384-391.]
[21]Zhang F,Mi Z Y.Advance in molecular biology of animal mitochondrial DNA[J].Progress in Biotechnology,1998,18(3):25-31.[张方,米志勇.动物线粒体DNA的分子生物学研究进展[J].生物工程进展,1998,18(3):25-31.]
[22]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.[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.]
[23]Brown W M,Prager E M,Wang A,et al.Mitochondrial DNAsequences of primates:tempo and mode of evolution[J].Journal of Molecular Evolution,1982,18(4):225-239.
[24]Wolstenholme D R,Jeon K W.Mitochondrial Genomes[M].San Diego:Academic Press,1992:22.
[25]Gao X G,Lu Z C,Tian J S,et al.Analysis and comparison of complete mitochondrial genome in spotted seal Phoca largha[J].Fisheries Science,2017,36(4):509-513.[高祥刚,鹿志创,田甲申,等.斑海豹线粒体基因组序列分析及比较研究[J].水产科学,2017,36(4):509-513.]
[26]Guo X H,Liu S J,Liu Q,et al.New progresses on mitochondrial DNA in fish[J].Acta Genetica Sinica,2004,31(9):983-1000.[郭新红,刘少军,刘巧,等.鱼类线粒体DNA研究新进展[J].遗传学报,2004,31(9):983-1000.]
[27]Premachandra H K A,la Cruz F L,Takeuchi Y,et al.Genomic DNA variation confirmed Seriola lalandi comprises three different populations in the Pacific,but with recent divergence[J].Scientific Reports,2017,7:Article No.9386.
[28]Zhang L L,Cheng Q Q.Mitochondrial genome characteristics and phylogenetic information of family Engraulidae(Clupeiformes:Clupeoidei)fishes[J].Marine Fisheries,2012,34(1):7-14.[张丽丽,程起群.鳀科鱼类线粒体全基因组序列结构特征及系统发育信息分析[J].海洋渔业,2012,34(1):7-14]
[29]He H Y,Yu W D,Jiang W B.Research progress in mitochondrial genomics of butterflie[J].Chinese Bulletin of Life Sciences,2016,28(9):978-985.[何海燕,俞伟东,蒋韦斌.蝶类线粒体基因组学研究进展[J].生命科学,2016,28(9):978-985.]
[30]Zhu S H,Zheng W J,Zou J X,et al.Mitochondrial DNAcontrol region structure and molecular phylogenetic relationship of Carangidae[J].Zoological Research,2007,28(6):606-614.[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.]
[2]Liu S F,Wu R X,Zhu L,et al.Complete sequence and gene organization of mitochondrial DNA of the small yellow croaker Larimichthys polyactis[J].Oceanologia et Limnologia Sinica,2010,41(6):885-894.[柳淑芳,吴仁协,朱玲,等.小黄鱼(Larimichthys polyactis)线粒体基因组结构与特征[J].海洋与湖沼,2010,41(6):885-894.]
[3]He C B,Gao X G,Wang X M,et al.Structure and evolution of complete mitochondrial genome of spotted halibut Verasper variegatus[J].Journal of Fishery Sciences of China,2007,14(4):584-592.[赫崇波,高祥刚,王效敏,等.圆斑星鲽线粒体基因组全序列结构及其进化[J].中国水产科学,2007,14(4):584-592.]
[4]Mao M G,Gu J,Liu R T,et al.Analysis of complete mitochondrial genome sequences of Gadus macrocephalus[J/OL].Acta Hydrobiologica Sinica,2018(06-18)/[2018-9-6].http://kns.cnki.net/kcms/detail/42.1230.Q.20180618.2206.002.html.[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/OL].水生生物学报,2018(06-18)/[2018-9-6].http://kns.cnki.net/kcms/detail/42.1230.Q.20180618.2206.002.html.]
[5]Huang X L,Yang Y K,Lin H Z,et al.Phylogenetic informantion analysis of mitochondrial genome sequences in Siganus(Perciformes:Siganidae)[J].Journal of Biology,2018,53(2):207-219.[黄小林,杨育凯,林黑着,等.篮子鱼属线粒体基因组序列系统发育信息分析[J].生物学杂志,2018,53(2):207-219.]
[6]Jiang Z L,Zhang M,Lin Y,et al.Complete mitochondrial genome sequence and phylogenetic analysis of Oreochromis aureus[J].Journal of Fishery Sciences of China,2011,18(4):790-800.[蒋宗良,张明,林勇,等.奥利亚罗非鱼线粒体基因组全序列测定与系统进化分析[J].中国水产科学,2011,18(4):790-800.]
[7]Yang Y,Song X J,Tang W Q,et al.Complete mitochondrial genome of Acrossocheilus kreyenbergii,with phylogenetic analysis of genus Acrossocheilus[J].Chinese Journal of Zoology,2018,53(2):207-219.[杨杨,宋小晶,唐文乔,等.克氏光唇鱼线粒体基因组测定及光唇鱼属的系统发育分析[J].动物学杂志,2018,53(2):207-219.]
[8]Schuster S C.Next-generation sequencing transforms today’s biology[J].Nature Methods,2008,5:16-18.
[9]Li R,Xu Y J,Liu X Z,et al.Morphometric analysis and internal anatomy of yellowtail kingfish(Seriola aureovittata)[J].Progress in Fishery Sciences,2017,38(1):142-149.[李荣,徐永江,柳学周,等.黄条鰤(Seriola aureovittata)形态度量与内部结构特征[J].渔业科学进展,2017,38(1):142-149.]
[10]Quéro J C,Hureau J C,Post A,et al.Check-list of the fishes of the eastern tropical Atlantic[J].Reviews in Fish Biology and Fisheries,1992,2(2):182-184.
[11]Iguchi J,Takashima Y,Namikoshi A,et al.Species identification method for marine products of Seriola and related species[J].Fisheries Science,2012,78(1):197-206.
[12]Martinez-Takeshita N,Purcell C M,Chabot C L,et al.A tale of three tails:Cryptic speciation in a globally distributed marine fish of the genus,Seriola[J].Copeia,2015,103(2):357-368.
[13]Shi B,Liu Y S,Liu X Z,et al.Study on the karyotype of yellowtail kingfish(Seriola aureovittata)[J].Progress in Fishery Sciences,2017,38(1):136-141.[史宝,刘永山,柳学周,等.黄条鰤(Seriola aureovittata)染色体核型分析[J].渔业科学进展,2017,38(1):136-141.]
[14]Meng Q W,Su J X,Miao X Z.Systematics of Fishes[M].Beijing:China Agriculture Press,1995:672-673.[孟庆闻,苏锦祥,缪学祖.鱼类分类学[M].北京:中国农业出版社,1995:672-673.]
[15]Balanov A A.On the species composition of fish of the genus Seriola(Carangidae)in the northwestern part of the Sea of Japan[J].Journal of Ichthyology,2008,48(6):415-421.
[16]Beaumont A.Genetics and evolution of aquatic organisms[J].Reviews in Fish Biology and Fisheries,1995,5(3):385-386.
[17]Burland T G.DNASTAR’s Lasergene sequence analysis software[M]//Bioinformatics Methods and Protocols.Totowa:Humana Press,2000,132:71-91.
[18]Thompson J D,Gibson T J,Plewniak F,et al.The CLUSTAL_X windows interface:flexible strategies for multiple sequence alignment aided by quality analysis tools[J].Nucleic Acids Research,1997,25(24):4876-4882.
[19]Kumar S,Stecher G,Peterson D,et al.MEGA-CC:computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis[J].Bioinformatics,2012,28(20):2685-2686.
[20]Xiao W H,Zhang Y P.Genetics and evolution of mitochondrial DNA in fish[J].Acta Hydrobiologica Sinica,2000,24(4):384-391.[肖武汉,张亚平.鱼类线粒体DNA的遗传与进化[J].水生生物学报,2000,24(4):384-391.]
[21]Zhang F,Mi Z Y.Advance in molecular biology of animal mitochondrial DNA[J].Progress in Biotechnology,1998,18(3):25-31.[张方,米志勇.动物线粒体DNA的分子生物学研究进展[J].生物工程进展,1998,18(3):25-31.]
[22]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.[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.]
[23]Brown W M,Prager E M,Wang A,et al.Mitochondrial DNAsequences of primates:tempo and mode of evolution[J].Journal of Molecular Evolution,1982,18(4):225-239.
[24]Wolstenholme D R,Jeon K W.Mitochondrial Genomes[M].San Diego:Academic Press,1992:22.
[25]Gao X G,Lu Z C,Tian J S,et al.Analysis and comparison of complete mitochondrial genome in spotted seal Phoca largha[J].Fisheries Science,2017,36(4):509-513.[高祥刚,鹿志创,田甲申,等.斑海豹线粒体基因组序列分析及比较研究[J].水产科学,2017,36(4):509-513.]
[26]Guo X H,Liu S J,Liu Q,et al.New progresses on mitochondrial DNA in fish[J].Acta Genetica Sinica,2004,31(9):983-1000.[郭新红,刘少军,刘巧,等.鱼类线粒体DNA研究新进展[J].遗传学报,2004,31(9):983-1000.]
[27]Premachandra H K A,la Cruz F L,Takeuchi Y,et al.Genomic DNA variation confirmed Seriola lalandi comprises three different populations in the Pacific,but with recent divergence[J].Scientific Reports,2017,7:Article No.9386.
[28]Zhang L L,Cheng Q Q.Mitochondrial genome characteristics and phylogenetic information of family Engraulidae(Clupeiformes:Clupeoidei)fishes[J].Marine Fisheries,2012,34(1):7-14.[张丽丽,程起群.鳀科鱼类线粒体全基因组序列结构特征及系统发育信息分析[J].海洋渔业,2012,34(1):7-14]
[29]He H Y,Yu W D,Jiang W B.Research progress in mitochondrial genomics of butterflie[J].Chinese Bulletin of Life Sciences,2016,28(9):978-985.[何海燕,俞伟东,蒋韦斌.蝶类线粒体基因组学研究进展[J].生命科学,2016,28(9):978-985.]
[30]Zhu S H,Zheng W J,Zou J X,et al.Mitochondrial DNAcontrol region structure and molecular phylogenetic relationship of Carangidae[J].Zoological Research,2007,28(6):606-614.[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.]
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