Journal of Tropical Oceanography >
Characterization of mitochondrial control region sequence of Psettodes erumei and phylogenetic analysis of Pleuronectiformes
Received date: 2009-01-23
Revised date: 2009-05-27
Online published: 2010-12-15
Supported by
国家自然科学基金项目（30870283）
Complete control region (CR) of Psettodes erumei mitochondrial genome was determined. Its size is 1,601 bp in length, with a 56 bp tandem repeat at 5’ end and a 8 bp one at 3’ end. Based on the alignment of CR sequences in this species and seven other flatfishes, three domains (the termination associated sequence domain, TAS; the central conserved domains, CSB-F, CSB-E, CSB-D and the conserved sequence block domains, CSB-1, CSB-2, CSB-3) and a Poly-T tract are identified. The difference of base composition of complete CR sequences is greater than that of CR sequence without repeated regions among eight flatfishes, and the variation coefficient of the former is about twice of the latter, which is mainly due to the het-erogenicity as length, base composition and copy numbers of repeated regions. With Carangoides armatus as the outgroup, the molecular phylogenetic relationship of 12 flatfishes was analyzed using the ML and BI methods. The results showed that P. erumei is the most primitive species among the flatfishes. Soleoidei and Pleuronectoidei are clustered into one clade, and then Psettodoidei merges to it. These results are consistent with that based on the morphological analyses.
Key words： mitochondrial DNA; control region; Psettodes erumei; phylogenesis; Pleuronectiformes
ZHANG Yan-chun,KONG Xiao-yu,WANG Zhong-ming . Characterization of mitochondrial control region sequence of Psettodes erumei and phylogenetic analysis of Pleuronectiformes[J]. Journal of Tropical Oceanography, 2010 , 29(6) : 71 -78 . DOI: 10.11978/j.issn.1009-5470.2010.06.071
[1] 李思忠, 王惠民. 中国动物志——硬骨鱼纲 鲽形目 [M].北京: 科学出版社, 1995.
[2] 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.
[3] FUMAGALLI L, TABERLET P, FAVRE L, et al. Origin and evolution of homologous repeated sequences in the mitochondrial DNA control region of shrews [J]. Mol Biol Evol, 1996, 13(1): 31—46.
[4] 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.
[5] SAITOH K, HAYASHIZAKI K, YOKOYAMA Y, et al. Complete nucleotide sequence of Japanese flounder (Paralichthys olivaceus) mitochondrial genome: structural properties and cue for resolving teleostean relationships [J]. J Hered, 2000, 91(4): 271-278.
[6] HOARAU G, HOLLA S, LESCASSE R, et al. Heteroplasmy and evidence for recombination in the mitochondrial control region of the flatfish Platichthys flesus [J]. Mol Biol Evol, 2002, 19(12): 2261-2264.
[7] MANCHADO M, CATANESE G, PONCE M, et al. The complete mitochondrial genome of the
[8] HE CHONGBO, HAN JIABO, GE LONGLI, et al. Sequence and organization of the complete mitochondrial genomes of spotted halibut (Verasper variegatus) and barfin flounder (Verasper moseri) [J]. DNA Seq, 2008, 19(3): 246-255.
[9] MJELLE K A, KARLSEN B O, JORGENSEN T E, et al. Halibut mitochondrial genomes contain extensive heteroplasmic tandem repeat arrays involved in DNA recombination [J]. BMC Genomics, 2008, 9(10): 1-11
[10] FABER J E, STEPIEN C A. Tandemly Repeated sequences in the mitochondrial DNA control region and phylogeography of the pike-perches Stizostedion [J]. Mol Phylogenet Evol, 1998, 10(3): 310-322.
[11] NESBO C L, ARAB M O, JAKOBSEN K S. Heteroplasmy, length and sequence variation in the mtDNA control regions of three percid fish species (Perca fluviatilis, Acerina cernua, Stizostedion lucioperca) [J]. Genetics, 1998, 148: 1907-1919.
[12] 张四明, 吴清江, 张亚平. 中华鲟(Acipenser sinensis)及相关种类的mtDNA控制区串联重复序列及其进化意义[J]. 中国生物化学与分子生物学报, 2000, 16(4): 458-461.
[13] SELL J, SPIRKOVSKI Z. Mitochondrial DNA diferentiation between two forms of trout Salmo letnica, endemic to the Balkan Lake Ohrid reflects their reproductive isolation [J]. Molecular Ecology, 2004, 13: 3633-3644.
[14] YUE GENHUA, LIEW W C, ORBAN L. The complete mitochondrial genome of a basal teleost, the Asian arowana (Scleropages formosus, Osteoglossidae) [J]. BMC Genomics, 2006, 7(242): 1-13.
[15] 唐文乔, 胡雪莲, 杨金权. 从线粒体控制区全序列变异看短颌鲚和湖鲚的物种有效性[J]. 生物多样性, 2007, 15(3): 224-231.
[16] SBISA 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: 125-140.
[17] BROUGHTON R E, DOWLING T E. Length variation in mitochondrial DNA of the minnow Cyprinella spiloptera [J]. Genetics, 1994, 138(1): 179-190.
[18] LEE J S, MIYA M, LEE Y S, et al. The complete DNA sequence of the mitochondrial genome of the self-fertilizing fish Rivulus marmoratus (Cyprinodontiformes, Rivulidae) and the first description of duplication of a control region in fish [J]. Gene, 2001, 280: 1-7.
[19] GRUNWALD C, STABILE J, WALDMAN J R, et a1. Population genetics of shortnose sturgeon Acipenser brevirostrum based on mitochondrial DNA control region sequences [J]. Mol Ecol, 2002, 11(10): 1885-1898.
[20] RAVAGO R G, MONJE V D, JUINIO-MENEZ M A. Length and sequence variability in mitochondrial control region of the Milkfish, Chanos chanos [J]. Mar Biotechnol, 2002, 4: 40-50.
[21] ABBOT C L, DOUBLE M C, TRUEMAN J W H, et al. An unusual source of apparent mitochondrial heteroplasmy: duplicate mitochondrial control regions in Thalassarche albatrosses [J]. Mol Ecol, 2005, 14: 3605-3613.
[22] ZHAO JINLIANG, WANG WEIWEI, LI SIFA, et al. Structure of the mitochondrial DNA control region of the sinipercine fishes and their phylogenetic relationship [J]. Acta Genetica Sinica, 2006, 33(9): 793-799.
[23] 谢振宇, 杜继曾, 陈学群, 等.线粒体控制区在鱼类种内遗传分化中的意义[J]. 遗传，2006, 28(3): 362-368.
[24] SAMBROOK J, FRITSCH E F, MANIATIS T. Molecular cloning [M]//A Laboratory Manual, 2nd ed.
[25] TAMURA K, DUDLEY J, NEI M, et al. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0 [J]. Mol. Biol Evol, 2007, 24(8): 1596-1599.
[26] MATHEWS D H, DISNEY M D, CHILDS J L, et al. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure [J]. Proceedings of the National Academy of Sciences USA, 2004, 10: 7287-7292.
[27] POSADA D, CRANDALL K A. Modeltest: testing the model of DNA substitution [J]. Bioinformatics, 1998, 14: 817-818.
[28] GUINDON S, GASCUEL O. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood [J]. Syst Biol , 2003, 52(5): 696-704.
[29] RONQUIST F, HUELSENBECK J P. Mrbayes 3: Bayesian phylogenetic inference under mixed models [J]. Bioinformatics, 2003, 19: 1572-1574.
[30] METROPOLIS N, ROSRNBLUTH A W, ROSENBLUTH M N, et al. Equations of state calculations by fast computing machines [J]. Chem Phys, 1953, 21(6): 1087-1091.
[31] HASTINGS W K. Monte carlo sampling methods using Markov chains and their applications[J]. Biometrika, 1970, 57(1): 97-109.
[32] SACCONE C, PESOLE G, SBISA E. The main regulatory region of mammalian mitochondrial DNA: Structure-function model and evolutionary pattern [J]. J Mol Evo1, 1991, 33: 83-91.
[33] LEE W J, CONROY J, HOWELL W H, et al. Structure and evolution of teleost mitochondrial control regions [J]. J Mol Evol, 1995, 41(1): 54-66.
[34] 刘焕章. 鱼类线粒体DNA控制区的结构与进化: 以鲚鲅鱼类为例[J].自然科学进展, 2002,12(3): 266-270.
[35] WANG WEI, HE SHUNPING, CHEN YIYU. Mitochondrial d-loop sequence variation and phylogeny of gobiobotine fishes [J]. Progress Nat Sci, 2002, 12(11): 866-868.
[36] 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.
[37] MIYA M,
[38] 刘海, 杨光, 魏辅文, 等. 中国大陆梅花鹿 mtDNA控制区序列变异及种群遗传结构分析[J]. 动物学报, 2003, 49(1): 53-60.
[39] NORMAN J R. A systematic monograph of the flatfishes (Heterosomata), 1. Psettodidae, Bothidae, Pleuronectidae[M].
[40] CHAPLEAU F. Pleuronectiform relationships: A cladistic reassessment [J]. Bull Mar Sci, 1993, 52: 516-540.
[41] AHLSTROM E H, AMAOKA A K, HENSLEY D A, et al. Pleuronectiformes development [M]//MOSER H G, RICHARDS W J, COHEN D M, et al. Ontogeny and Systematic of Fishes. Special Publication n. 1. American Society of Ichthyology and Herpertology,
[42] AZEVEDO M F C, OLIVEIRA C, PARDO B G, et a1. Phylogenetic analysis of the order Pleuronectiformes (Teleostei) based on sequences of 12S and 16S mitochondrial genes [J]. Genetics and Molecular Biology, 2008, 31(1): 284-292.
[43] YOU FENG, LIU JING, ZHANG PEIJUN, et a1. Preliminary study on mitochondrial 16S rRNA gene sequences and phylogeny of flatfishes(Pleuronectiformes) [J]. Chinese Journal of Oceanology and Limnology, 2005, 23(3): 335-339.
[44] PARDO B, MACHORDOM A, FORESTI F, et a1. Phylogenetic analysis of flatfish (Order Pleuronectiformes) based on mitochondrial 16s rDNA sequences [J]. SCI MAR, 2005, 69(4): 531-543.
[45] KARTAVTSEV Y P, PARK T J, VINNIKOV K A, et a1. Cytochrome b (Cyt-b) gene sequence analysis in six flatfish species (Teleostei, Pleuronectidae), with phylogenetic and taxonomic insights [J]. Mar Biol, 2007, 152: 757-773.
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