吸虫类线粒体基因组的特征及系统发生分析
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摘要
本研究分析了吸虫纲下单殖亚纲的13个物种和复殖亚纲的37个物种,共50个物种的线粒体全基因组序列,旨在揭示吸虫类线粒体基因组的主要基本特征,探究吸虫纲物种的系统发生关系。吸虫类的线粒体基因组具有明显的A+T含量偏向性。吸虫类的12个蛋白质编码基因和两个核糖体RNA基因的变异程度很大,其变异比例在48.8%到92.0%之间。根据线粒体基因组的12个蛋白质编码基因和两个核糖体RNA基因的差异位点分析,建议采用ND5、CYTB和ND4基因作为16S、12S和COⅠ基因的辅助分子标记。吸虫类各物种的线粒体基因组出现了大量的基因重排现象,除鸮形目裂体科和多后盘目外,其余物种均遵循类似的基因排列顺序。线粒体基因组的系统发育结果强烈支持将单殖亚纲提升到单殖纲,并支持将目前分类地位未定的腹盘科野牛平腹吸虫归入斜睾目同盘总科。本研究将为吸虫类线粒体基因组的研究、分子进化和分子诊断等方面提供诸多信息,并在今后的实践应用中起到一定的指导作用。
In this paper, the mitochondrial genome sequences of 50 species of 13 Monogenea species and 37 Digenea species of trematoda were analyzed, aiming at revealing the basic characteristics of trematoda mitochondrial genome sequences, and exploring the phylogenetic relationship of the trematoda species. The trematodes' mitochondrialgenome had obvious A+T content bias. The 12 protein coding genes and 2 ribosomal RNA genes of trematodes varied a lot, the proportion of variance was between 48.8% and 92.0%. According to the differential site analysis of 12 protein coding genes and 2 ribosomal RNA genes in mitochondrial genome, ND5, CYTB and ND4 genes were suggested as auxiliary molecular markers for 16 S, 12 S and COI genes. Mitochondrial genomes of trematode species showed a large number of gene rearrangements sequences, and except for the Strigiformes Schistosomatidae and Polyopisthocotylea, the rest of the species followed a similar gene sequence. Phylogenetic results of mitochondrial genomes strongly supported that Monogenea should be promoted to Monogenoidea, and suggested that the Gastrodiscidae Homalogaster paloniae, which has not been classified at present, should be categorized into Plagiorchiida, Paramphistomidae. This paper would provide a lot of information for the research of trematoda mitochondrial genomes, molecular evolution and molecular diagnosis and would play a guiding role in the future practice of application as well.
In this paper, the mitochondrial genome sequences of 50 species of 13 Monogenea species and 37 Digenea species of trematoda were analyzed, aiming at revealing the basic characteristics of trematoda mitochondrial genome sequences, and exploring the phylogenetic relationship of the trematoda species. The trematodes' mitochondrialgenome had obvious A+T content bias. The 12 protein coding genes and 2 ribosomal RNA genes of trematodes varied a lot, the proportion of variance was between 48.8% and 92.0%. According to the differential site analysis of 12 protein coding genes and 2 ribosomal RNA genes in mitochondrial genome, ND5, CYTB and ND4 genes were suggested as auxiliary molecular markers for 16 S, 12 S and COI genes. Mitochondrial genomes of trematode species showed a large number of gene rearrangements sequences, and except for the Strigiformes Schistosomatidae and Polyopisthocotylea, the rest of the species followed a similar gene sequence. Phylogenetic results of mitochondrial genomes strongly supported that Monogenea should be promoted to Monogenoidea, and suggested that the Gastrodiscidae Homalogaster paloniae, which has not been classified at present, should be categorized into Plagiorchiida, Paramphistomidae. This paper would provide a lot of information for the research of trematoda mitochondrial genomes, molecular evolution and molecular diagnosis and would play a guiding role in the future practice of application as well.
引文
Arnason U.,Gullberg A.,Janke A.,and Kullberg M.,2007,Mitogenomic analyses of caniform relationships,Molecular Phylogenetics and Evolution,45(3):863-874
Bai J.,Zhu C.C.,Nie Z.H.,Wang Y.,and Zhou X.M.,2016,Introduction and comparative analysis of brachyura mitochondrial genomes research,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(10):2627-2639(白俊,朱春潮,聂宗恒,邹节新,汪雁,周宪民,2016,短尾类线粒体基因组研究概要及比较分析,基因组学与应用生物学,35(10):2627-2639)
Boore J.L.,1999,Animal mitochondrial genome,Nucleic Acids Research,27(8):1767-1780
Briscoe A.G.,Bray R.A.,Brabec J.,and Littlewood D.T.,2016,The mitochondrial genome and ribosomal operon of Brachycladium goliath(Digenea:Brachycladiidae)recovered from a stranded minke whale,Parasitology International,65(3):271-275
Cao X.M.,and Wang D.B.,1991,The life history of homalogaster paloniae poirier,1882(termatoda:gastrodiscidae),Dongwu Xuebao(Current Zoology),37(2):168-176(曹小明,汪涤邦,1991,野牛平腹吸虫的生活史研究,动物学报,37(2):168-176)
Chen X.T.,1956,Taxonomy of trematodes from China(families and genera),Dongwu Xuebao(Current Zoology),8(1):101-120(陈心陶,1956,中国吸虫的分类(科与属),动物学报,8(1):101-120)
Cui A.L.,Chang Z.S.,Chen M.G.,Blair D.,Chen S.H.,Zhang Y.N.,and Feng Z.,2003,Taxonomic status of paragonimus skrjabini populations from five provinces in China in morpho logy,Zhongguo Dongwu Chuanranbing Xuebao(Chinese Journal of Veterinary Parasitology),11(1):4-7(崔爱利,常正山,陈名刚,David Blair,陈韶红,张永年,冯正,2003,我国五省斯氏并殖吸虫群体形态学的分类地位研究,中国动物传染病学报,11(1):4-7)
Dorny P.,Praet N.,Deckers N.,and Gabriel S.,2009,Emerging food-borne parasites,Veterinary Parasitology,163(3):196-206
Guindon S.,Dufayard J.F.,Lefort V.,Anisimova M.,Hordijk W.,and Gascuel O.,2010,New algorithms and methods to estimate maximum likelihood phylogenies:assessing the perfor mance of Phy ML 3.0,Systematic Biology,59(3):317-337
Hu M.,and Gasser R.B.,2006,Mitochondrial genomes of parasitic nematodes-progress and perspectives,Trends in Parasitology,22(2):78
Jeon H.K.,Kim K.H.,and Eom K.S.,2007,Complete sequence of the mitochondrial genome of Taenia saginata:comparison with T.solium and T.asiatica,Parasitology International,56(3):243
Jia W.Z.,Yan H.B.,Shi W.G.,Guo A.J.,and Zhan F.,2011,Research progress on complete mitochondrial genome sequences and their application for trematodes,Zhongguo Shouyi Xuebao(Chinese Journal of Veterinary Science),31(6):926-932(贾万忠,闫鸿斌,史万贵,郭爱疆,詹芳,2011,吸虫线粒体基因组及其应用研究进展,中国兽医学报,31(6):926-932)
Larkin M.A.,Blackshields G.,Brown N.P.,Chenna R.,McGettigan P.A.,McWilliam H.,Valentin F.,Wallace I.M.,Wilm A.,Lopez R.,Thompson J.D.,Gibson T.J.,and Higgins D.G.,2007,Clustal W and Clustal X version 2.0,Bioinformatics,23(21):2947-2948
Le T.H.,Blair D.,Agatsuma T.,Humair P.F.,Campbell N.J.H.,I-wagami M.,Littlewood D.T.,Peacock B.,Johnston D.A.,Bartley J.,Rollinson D.,Herniou E.A.,Zarlenga D.S.,and McManus D.P.,2000,Phylogenies inferred from mitochondrial gene orders-a cautionary tale from the parasitic flatworms,Molecular Biology&Evolution,17(7):1123-1125
Le T.H.,Blair D.,and Mcmanus D.P.,2002,Mitochondrial genomes of parasitic flatworms,Trends in Parasitology,18(5):206-213
Li M.W.,Zou F.C.,Lin R.Q.,and Zhu X.Q.,2005,Advance of studies on mitochondrial DNA of parasitic nematodes,Jishengchong Yu Yixue Kunchong Xuebao(Acta Parasitologica et Medica Entomologica Sinica),12(1):57-64(李明伟,邹丰才,林瑞庆,朱兴全,2005,寄生性线虫线粒体基因组研究进展,寄生虫与医学昆虫学报,12(1):57-64)
Littlewood D.T.,Lockyer A.E.,Webster B.L.,Johnston D.A.,and Le T.H.,2006,The complete mitochondrial genomes of Schistosoma haematobium and Schistosoma spindale and the evolutionary history of mitochondrial genome changes among parasitic flatworms,Molecular Phylogenetics&Evolution,39(2):452
Liu J.,Cheng X.J.,and Pan X.Z.,2015,Research advances in common food-borne trematodiases and their diagnosis and chemotherapy,Chuanranbing Xinxi(Infectious Disease Information),28(3):141-144(刘君,程训佳,潘孝彰,2015,常见食源性吸虫病及其诊治进展,传染病信息,28(3):141-144)
Mei X.F.,Yang L.,Tao L.,Li J.,and Wang D.Y.,2016,The sequencing and analysis of Homalogaster paloniae ITS2 gene isolated from black goat,Zhongguo Shouyi Zazhi(Chinese Journal of Veterinary Medicine),52(6):31-32(梅雪芳,杨磊,陶立,李健,黄维义,王冬英,2016,黑山羊源野牛平腹盘吸虫ITS2基因序列测定及分析,中国兽医杂志,52(6):31-32)
Nakao M.,Mcmanus D.P.,Schantz P.M.,Craig P.S.,and Ito A.,2007,A molecular phylogeny of the genus Echinococcus inferred from complete mitochondrial genomes,Parasitology,134(5):713
Niu Y.D.,Li M.,Wei F.W.,and Feng Z.J.,2001,Reliability of mt DNA as molecular marker and its perspective,Yichuan(Hereditas),23(6):593-598(牛屹东,李明,魏辅文,冯祚建,2001,线粒体DNA用作分子标记的可靠性和研究前景,遗传,23(6):593-598)
Robinson M.W.,and Dalton J.P.,2009,Zoonotic helminth infections with particular emphasis on fasciolosis and other trematodiases,Philosophical Transactions Biological Sciences,364(1530):2763-2376
Ronquist F.,Teslenko M.,Van d.M.P.,Ayres D.L.,Darling A.,Hohna S.,Larget B.,Liu L.,Suchard M.A.,and Huelsenbeck P.,2012,Mr Bayes 3.2:efficient Bayesian phylogenetic inference and model choice across a large model space,Systematic Biology,61(3):539
Rozas J.,Sanchez-Delbarrio J.C.,Messeguer X.,and Rozas R.,20 03,DnaSP,DNA polymorphism analyses by the coalescent and other methods,Bioinformatics,19(18):2496-2497
Tamura K.,Stecher G.,Peterson D.,Filipski A.,and Kumar S.,2013,MEGA6:molecular evolutionary genetics analysis version 6.0,Molecular Biology&Evolution,30(4):2725-2729
Tang C.T.,and Tang Z.Z.,eds.,2005,Trematology in China,Fujian science and technology publishing house,Fuzhou,China,pp.20-76(唐崇惕,唐仲璋,主编,2005,中国吸虫学,福建科学技术出版社,中国,福州,pp.20-76)
Vazquez G.E.,Ponzoni I.,and Brignole N.B.,2001,ModGen:a model generator for instrumentation analysis,Advances in Engineering Software,32(1):37-48
Von N.M.,Brown W.M.,and Boore J.L.,2001,Complete sequence of the mitochondrial genome of the tapeworm Hymenolepis diminuta:gene arrangements indicate that Platyhelminths are Eutrochozoans,Molecular Biology and Evolution,18(5):721-730
Xia X.Q.,and Wang W.J.,1997,The biology and ecology of monogenea,Shuisheng Shengwu Xuebao(Acta Hydrobiologica Sinica),21(1):75-84(夏晓勤,王伟俊,1997,单殖吸虫生物学及生态学,水生生物学报,21(1):75-84)
Xu C.Y.,Chen T.T.,Li S.,Cui D.Z.,Li P.,Ning L.H.,Li D.T.,Wang L.W.,Liu X.,Jiang C.,Ma X.,Zhang H.,and Chen H.,2015,Molecular characterization of the waxy maize key starch synthesis gene and development of molecular markers,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),13(3):531-540(徐春艳,陈亭亭,李松,崔德周,李鹏,宁丽华,李德涛,王莉雯,刘旭,姜川,马侠,张华,陈化榜,2015,糯玉米waxy基因序列特征分析及分子标记开发,分子植物育种,13(3):531-540)
Zhang J.,2011,The evolutionary study on monogeneans using m itochondrial genomes,Dissertation for Ph.D.,Sun Yat-sen University,Supervisor:Xie M.Q.,pp.1-26(张娟,2011,单殖吸虫线粒体基因组进化生物学研究,博士学位论文,中山大学,导师:谢明权,pp.1-26)
Zhao J.L.,and Li S.F.,2003,A survey of genomics study on Chinese mitten crab,Eriocheir sinensis,Jimeidaxue Xuebao(Ziran Kexue Ban)(Journal of Jimei University(Natural Science Edition)),8(4):311-316(赵金良,李思发,2003,中华绒螯蟹基因组研究概述,集美大学学报(自然科学版),8(4):311-316)
Bai J.,Zhu C.C.,Nie Z.H.,Wang Y.,and Zhou X.M.,2016,Introduction and comparative analysis of brachyura mitochondrial genomes research,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(10):2627-2639(白俊,朱春潮,聂宗恒,邹节新,汪雁,周宪民,2016,短尾类线粒体基因组研究概要及比较分析,基因组学与应用生物学,35(10):2627-2639)
Boore J.L.,1999,Animal mitochondrial genome,Nucleic Acids Research,27(8):1767-1780
Briscoe A.G.,Bray R.A.,Brabec J.,and Littlewood D.T.,2016,The mitochondrial genome and ribosomal operon of Brachycladium goliath(Digenea:Brachycladiidae)recovered from a stranded minke whale,Parasitology International,65(3):271-275
Cao X.M.,and Wang D.B.,1991,The life history of homalogaster paloniae poirier,1882(termatoda:gastrodiscidae),Dongwu Xuebao(Current Zoology),37(2):168-176(曹小明,汪涤邦,1991,野牛平腹吸虫的生活史研究,动物学报,37(2):168-176)
Chen X.T.,1956,Taxonomy of trematodes from China(families and genera),Dongwu Xuebao(Current Zoology),8(1):101-120(陈心陶,1956,中国吸虫的分类(科与属),动物学报,8(1):101-120)
Cui A.L.,Chang Z.S.,Chen M.G.,Blair D.,Chen S.H.,Zhang Y.N.,and Feng Z.,2003,Taxonomic status of paragonimus skrjabini populations from five provinces in China in morpho logy,Zhongguo Dongwu Chuanranbing Xuebao(Chinese Journal of Veterinary Parasitology),11(1):4-7(崔爱利,常正山,陈名刚,David Blair,陈韶红,张永年,冯正,2003,我国五省斯氏并殖吸虫群体形态学的分类地位研究,中国动物传染病学报,11(1):4-7)
Dorny P.,Praet N.,Deckers N.,and Gabriel S.,2009,Emerging food-borne parasites,Veterinary Parasitology,163(3):196-206
Guindon S.,Dufayard J.F.,Lefort V.,Anisimova M.,Hordijk W.,and Gascuel O.,2010,New algorithms and methods to estimate maximum likelihood phylogenies:assessing the perfor mance of Phy ML 3.0,Systematic Biology,59(3):317-337
Hu M.,and Gasser R.B.,2006,Mitochondrial genomes of parasitic nematodes-progress and perspectives,Trends in Parasitology,22(2):78
Jeon H.K.,Kim K.H.,and Eom K.S.,2007,Complete sequence of the mitochondrial genome of Taenia saginata:comparison with T.solium and T.asiatica,Parasitology International,56(3):243
Jia W.Z.,Yan H.B.,Shi W.G.,Guo A.J.,and Zhan F.,2011,Research progress on complete mitochondrial genome sequences and their application for trematodes,Zhongguo Shouyi Xuebao(Chinese Journal of Veterinary Science),31(6):926-932(贾万忠,闫鸿斌,史万贵,郭爱疆,詹芳,2011,吸虫线粒体基因组及其应用研究进展,中国兽医学报,31(6):926-932)
Larkin M.A.,Blackshields G.,Brown N.P.,Chenna R.,McGettigan P.A.,McWilliam H.,Valentin F.,Wallace I.M.,Wilm A.,Lopez R.,Thompson J.D.,Gibson T.J.,and Higgins D.G.,2007,Clustal W and Clustal X version 2.0,Bioinformatics,23(21):2947-2948
Le T.H.,Blair D.,Agatsuma T.,Humair P.F.,Campbell N.J.H.,I-wagami M.,Littlewood D.T.,Peacock B.,Johnston D.A.,Bartley J.,Rollinson D.,Herniou E.A.,Zarlenga D.S.,and McManus D.P.,2000,Phylogenies inferred from mitochondrial gene orders-a cautionary tale from the parasitic flatworms,Molecular Biology&Evolution,17(7):1123-1125
Le T.H.,Blair D.,and Mcmanus D.P.,2002,Mitochondrial genomes of parasitic flatworms,Trends in Parasitology,18(5):206-213
Li M.W.,Zou F.C.,Lin R.Q.,and Zhu X.Q.,2005,Advance of studies on mitochondrial DNA of parasitic nematodes,Jishengchong Yu Yixue Kunchong Xuebao(Acta Parasitologica et Medica Entomologica Sinica),12(1):57-64(李明伟,邹丰才,林瑞庆,朱兴全,2005,寄生性线虫线粒体基因组研究进展,寄生虫与医学昆虫学报,12(1):57-64)
Littlewood D.T.,Lockyer A.E.,Webster B.L.,Johnston D.A.,and Le T.H.,2006,The complete mitochondrial genomes of Schistosoma haematobium and Schistosoma spindale and the evolutionary history of mitochondrial genome changes among parasitic flatworms,Molecular Phylogenetics&Evolution,39(2):452
Liu J.,Cheng X.J.,and Pan X.Z.,2015,Research advances in common food-borne trematodiases and their diagnosis and chemotherapy,Chuanranbing Xinxi(Infectious Disease Information),28(3):141-144(刘君,程训佳,潘孝彰,2015,常见食源性吸虫病及其诊治进展,传染病信息,28(3):141-144)
Mei X.F.,Yang L.,Tao L.,Li J.,and Wang D.Y.,2016,The sequencing and analysis of Homalogaster paloniae ITS2 gene isolated from black goat,Zhongguo Shouyi Zazhi(Chinese Journal of Veterinary Medicine),52(6):31-32(梅雪芳,杨磊,陶立,李健,黄维义,王冬英,2016,黑山羊源野牛平腹盘吸虫ITS2基因序列测定及分析,中国兽医杂志,52(6):31-32)
Nakao M.,Mcmanus D.P.,Schantz P.M.,Craig P.S.,and Ito A.,2007,A molecular phylogeny of the genus Echinococcus inferred from complete mitochondrial genomes,Parasitology,134(5):713
Niu Y.D.,Li M.,Wei F.W.,and Feng Z.J.,2001,Reliability of mt DNA as molecular marker and its perspective,Yichuan(Hereditas),23(6):593-598(牛屹东,李明,魏辅文,冯祚建,2001,线粒体DNA用作分子标记的可靠性和研究前景,遗传,23(6):593-598)
Robinson M.W.,and Dalton J.P.,2009,Zoonotic helminth infections with particular emphasis on fasciolosis and other trematodiases,Philosophical Transactions Biological Sciences,364(1530):2763-2376
Ronquist F.,Teslenko M.,Van d.M.P.,Ayres D.L.,Darling A.,Hohna S.,Larget B.,Liu L.,Suchard M.A.,and Huelsenbeck P.,2012,Mr Bayes 3.2:efficient Bayesian phylogenetic inference and model choice across a large model space,Systematic Biology,61(3):539
Rozas J.,Sanchez-Delbarrio J.C.,Messeguer X.,and Rozas R.,20 03,DnaSP,DNA polymorphism analyses by the coalescent and other methods,Bioinformatics,19(18):2496-2497
Tamura K.,Stecher G.,Peterson D.,Filipski A.,and Kumar S.,2013,MEGA6:molecular evolutionary genetics analysis version 6.0,Molecular Biology&Evolution,30(4):2725-2729
Tang C.T.,and Tang Z.Z.,eds.,2005,Trematology in China,Fujian science and technology publishing house,Fuzhou,China,pp.20-76(唐崇惕,唐仲璋,主编,2005,中国吸虫学,福建科学技术出版社,中国,福州,pp.20-76)
Vazquez G.E.,Ponzoni I.,and Brignole N.B.,2001,ModGen:a model generator for instrumentation analysis,Advances in Engineering Software,32(1):37-48
Von N.M.,Brown W.M.,and Boore J.L.,2001,Complete sequence of the mitochondrial genome of the tapeworm Hymenolepis diminuta:gene arrangements indicate that Platyhelminths are Eutrochozoans,Molecular Biology and Evolution,18(5):721-730
Xia X.Q.,and Wang W.J.,1997,The biology and ecology of monogenea,Shuisheng Shengwu Xuebao(Acta Hydrobiologica Sinica),21(1):75-84(夏晓勤,王伟俊,1997,单殖吸虫生物学及生态学,水生生物学报,21(1):75-84)
Xu C.Y.,Chen T.T.,Li S.,Cui D.Z.,Li P.,Ning L.H.,Li D.T.,Wang L.W.,Liu X.,Jiang C.,Ma X.,Zhang H.,and Chen H.,2015,Molecular characterization of the waxy maize key starch synthesis gene and development of molecular markers,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),13(3):531-540(徐春艳,陈亭亭,李松,崔德周,李鹏,宁丽华,李德涛,王莉雯,刘旭,姜川,马侠,张华,陈化榜,2015,糯玉米waxy基因序列特征分析及分子标记开发,分子植物育种,13(3):531-540)
Zhang J.,2011,The evolutionary study on monogeneans using m itochondrial genomes,Dissertation for Ph.D.,Sun Yat-sen University,Supervisor:Xie M.Q.,pp.1-26(张娟,2011,单殖吸虫线粒体基因组进化生物学研究,博士学位论文,中山大学,导师:谢明权,pp.1-26)
Zhao J.L.,and Li S.F.,2003,A survey of genomics study on Chinese mitten crab,Eriocheir sinensis,Jimeidaxue Xuebao(Ziran Kexue Ban)(Journal of Jimei University(Natural Science Edition)),8(4):311-316(赵金良,李思发,2003,中华绒螯蟹基因组研究概述,集美大学学报(自然科学版),8(4):311-316)
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