Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies

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• 作者：Wang Minxiao (1) (2)
  Sun Song (1)
  Li Chaolun (1)
  Shen Xin (3)
  
• 刊名：BMC Genomics
• 出版年：2011
• 出版时间：December 2011
• 年：2011
• 卷：12
• 期：1
• 全文大小：2621KB
• 参考文献：1. Humes AG: How Many Copepods. / Hydrobiologia 1994, 293:1鈥?. CrossRef
  2. Mauchline J: / The Biology of Calanoid Copepods. Academic Press, London; 1998:710.
  3. Huys Rony, Boxshall GA: / Copepod evolution. / Volume 159. Ray Society; 1991.
  4. Martin JW, Davis GE: An updated classification of the recent Crustacea. / History Museum of Los Angeles County: Los Angeles, CA (USA) VII 2001, 123. Science Series 39
  5. Dussart BH: A propos du r茅pertoire mondial des Calano茂des des eaux continentales. / Crustaceana 1984, 25鈥?1.
  6. Ho JS: Copepod Phylogeny - a Reconsideration of Huys-and-Boxhall Parsimony Versus Homology. / Hydrobiologia 1994, 293:31鈥?9. CrossRef
  7. Boxshall G, Halsey S: An introduction to copepod diversity. / 2004: Ray Soc 2004.
  8. Jenner RA: Higher-level crustacean phylogeny: Consensus and conflicting hypotheses. / Arthropod Struct Dev 2010,39(2鈥?):143鈥?53. CrossRef
  9. Wolstenholme DR: Animal Mitochondrial-DNA - Structure and Evolution. / International Review of Cytology-a Survey of Cell Biology 1992, 141:173鈥?16.
  10. Boore JL: Animal mitochondrial genomes. / Nucleic Acids Res 1999,27(8):1767鈥?780. CrossRef
  11. Boore JL, Fuerstenberg SI: Beyond linear sequence comparisons: the use of genome-level characters for phylogenetic reconstruction. / Philosophical transactions of the Royal Society of London 2008,363(1496):1445鈥?451. CrossRef
  12. Park JK, Choe BL, Eom KS: Two mitochondrial lineages in Korean freshwater Corbicula (Corbiculidae: Bivalvia). / Molecules and Cells 2004,17(3):410鈥?14.
  13. Nuwer M, Frost B, Armbrust EV: Population structure of the planktonic copepod Calanus pacificus in the North Pacific Ocean. / Marine Biology 2008,156(2):107鈥?15. CrossRef
  14. Burton RS, Byrne RJ, Rawson PD: Three divergent mitochondrial genomes from California populations of the copepod Tigriopus californicus. / Gene 2007,403(1鈥?):53鈥?9. CrossRef
  15. Simon C, Buckley TR, Frati F, Stewart JB, Beckenbach AT: Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. / Annual Review of Ecology Evolution and Systematics 2006, 37:545鈥?79. CrossRef
  16. Hassanin A: Phylogeny of Arthropoda inferred from mitochondrial sequences: Strategies for limiting the misleading effects of multiple changes in pattern and rates of substitution. / Mol Phylogenet Evol 2006,38(1):100鈥?16. CrossRef
  17. Place AR, Feng XJ, Steven CR, Fourcade HM, Boore JL: Genetic markers in blue crabs (Callinectes sapidus) II. Complete mitochondrial genome sequence and characterization of genetic variation. / Journal of Experimental Marine Biology and Ecology 2005,319(1鈥?):15鈥?7. CrossRef
  18. Machida RJ, Miya MU, Nishida M, Nishida S: Complete mitochondrial DNA sequence of Tigriopus japonicus (Crustacea: Copepoda). / Marine Biotechnology 2002,4(4):406鈥?17. CrossRef
  19. Jung SO, Lee YM, Park TJ, Park HG, Hagiwara A, Leung KMY, Dahms HU, Lee W, Lee JS: The complete mitochondrial genome of the intertidal copepod Tigriopus sp (Copepoda, Harpactidae) from Korea and phylogenetic considerations. / Journal of Experimental Marine Biology and Ecology 2006,333(2):251鈥?62. CrossRef
  20. Tjensvoll K, Hodneland K, Nilsen F, Nylund A: Genetic characterization of the mitochondrial DNA from Lepeophtheirus salmonis (Crustacea: Copepoda). A new gene organization revealed. / Gene 2005,353(2):218鈥?30. CrossRef
  21. Ki JS, Park HG, Lee JS: The complete mitochondrial genome of the cyclopoid copepod Paracyclopina nana: A highly divergent genome with novel gene order and atypical gene numbers. / Gene 2009,435(1鈥?):13鈥?2. CrossRef
  22. Uye S: Why does Calanus sinicus prosper in the shelf ecosystem of the Northwest Pacific Ocean? / Ices J Mar Sci 2000,57(6):1850鈥?855. CrossRef
  23. Machida RJ, Miya MU, Nishida M, Nishida S: Large-scale gene rearrangements in the mitochondrial genomes of two calanoid copepods Eucalanus bungii and Neocalanus cristatus (Crustacea), with notes on new versatile primers for the srRNA and COI genes. / Gene 2004, 332:71鈥?8. CrossRef
  24. Hassanin A, Leger N, Deutsch J: Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of metazoa, and consequences for phylogenetic inferences. / Systematic biology 2005,54(2):277鈥?98. CrossRef
  25. Kilpert F, Podsiadlowski L: The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda) bears a novel gene order and unusual control region features. / Bmc Genomics 2006., 7:
  26. Clayton DA: Transcription and replication of mitochondrial DNA. / Human reproduction (Oxford, England) 2000,15(Suppl 2):11鈥?7.
  27. Xu W, Jameson D, Tang B, Higgs PG: The relationship between the rate of molecular evolution and the rate of genome rearrangement in animal mitochondrial genomes. / Journal of Molecular Evolution 2006,63(3):375鈥?92. CrossRef
  28. Ruiz-Trillo I, Riutort M, Fourcade HM, Baguna J, Boore JL: Mitochondrial genome data support the basal position of Acoelomorpha and the polyphyly of the Platyhelminthes. / Mol Phylogenet Evol 2004,33(2):321鈥?32. CrossRef
  29. Gutell RR: Collection of Small-Subunit (16s- and 16s-Like) Ribosomal-Rna Structures - 1994. / Nucleic Acids Res 1994,22(17):3502鈥?507. CrossRef
  30. De Rijk P, Robbrecht E, de Hoog S, Caers A, Van de Peer Y, De Wachter R: Database on the structure of large subunit ribosomal RNA. / Nucleic Acids Research 1999,27(1):174鈥?78. CrossRef
  31. Crease TJ: The complete sequence of the mitochondrial genome of Daphnia pulex (Cladocera: Crustacea). / Gene 1999,233(1鈥?):89鈥?9. CrossRef
  32. Van de Peer Y, De Rijk P, Wuyts J, Winkelmans T, De Wachter R: The European Small Subunit Ribosomal RNA database. / Nucleic Acids Research 2000,28(1):175鈥?76. CrossRef
  33. Domes K, Maraun M, Scheu S, Cameron SL: The complete mitochondrial genome of the sexual oribatid mite Steganacarus magnus: genome rearrangements and loss of tRNAs. / Bmc Genomics 2008., 9:
  34. Segawa RD, Aotsuka T: The mitochondrial genome of the Japanese freshwater crab, Geothelphusa dehaani (Crustacea: Brachyura): Evidence for its evolution via gene duplication. / Gene 2005, 355:28鈥?9. CrossRef
  35. Shao RF, Barker SC, Mitani H, Takahashi M, Fukunaga M: Molecular mechanisms for the variation of mitochondrial gene content and gene arrangement among chigger mites of the genus Leptotrombidium (Acari: Acariformes). / Journal of Molecular Evolution 2006,63(2):251鈥?61. CrossRef
  36. Dermauw W, Van Leeuwen T, Vanholme B, Tirry L: The complete mitochondrial genome of the house dust mite Dermatophagoides pteronyssinus (Trouessart): a novel gene arrangement among arthropods. / Bmc Genomics 2009., 10:
  37. Ogoh K, Ohmiya Y: Complete mitochondrial DNA sequence of the sea-firefly, Vargula hilgendorfii (Crustacea, Ostracoda) with duplicate control regions. / Gene 2004,327(1):131鈥?39. CrossRef
  38. Mwinyi A, Meyer A, Bleidorn C, Lieb B, Bartolomaeus T, Podsiadlowski L: Mitochondrial genome sequence and gene order of Sipunculus nudus give additional support for an inclusion of Sipuncula into Annelida. / Bmc Genomics 2009., 10:
  39. Jang KH, Hwang UW: Complete mitochondrial genome of Bugula neritina (Bryozoa, Gymnolaemata, Cheilostomata): phylogenetic position of Bryozoa and phylogeny of lophophorates within the Lophotrochozoa. / Bmc Genomics 2009., 10:
  40. Kurabayashi A, Ueshima R: Complete sequence of the mitochondrial DNA of the primitive opisthobranch gastropod Pupa strigosa: systematic implication of the genome organization. / Mol Biol Evol 2000,17(2):266鈥?77.
  41. Lavrov DV, Brown WM, Boore JL: Phylogenetic position of the Pentastomida and (pan)crustacean relationships. / P Roy Soc Lond B Bio 2004,271(1538):537鈥?44. CrossRef
  42. Zhang DX, Hewitt GM: Insect mitochondrial control region: A review of its structure, evolution and usefulness in evolutionary studies. / Biochemical Systematics and Ecology 1997,25(2):99鈥?20. CrossRef
  43. Taanman JW: The mitochondrial genome: structure, transcription, translation and replication. / Biochimica Et Biophysica Acta-Bioenergetics 1999,1410(2):103鈥?23. CrossRef
  44. Saito S, Tamura K, Aotsuka T: Replication origin of mitochondrial DNA in insects. / Genetics 2005,171(4):1695鈥?705. CrossRef
  45. Garesse R, Kaguni LS: A Drosophila model of mitochondrial DNA replication: Proteins, genes and regulation. / Iubmb Life 2005,57(8):555鈥?61. CrossRef
  46. Belinky F, Rot C, Ilan M, Huchon D: The complete mitochondrial genome of the demosponge Negombata magnifica (Poecilosclerida). / Mol Phylogenet Evol 2008,47(3):1238鈥?243. CrossRef
  47. Lavrov DV, Boore JL, Brown WM: The complete mitochondrial DNA sequence of the horseshoe crab Limulus polyphemus. / Molecular Biology and Evolution 2000,17(5):813鈥?24.
  48. Boore JL, Medina M, Rosenberg LA: Complete sequences of the highly rearranged molluscan mitochondrial genomes of the scaphopod Graptacme eborea and the bivalve Mytilus edulis. / Molecular Biology and Evolution 2004,21(8):1492鈥?503. CrossRef
  49. Yu ZN, Wei ZP, Kong XY, Shi W: Complete mitochondrial DNA sequence of oyster Crassostrea hongkongensis-a case of "Tandem duplication-random loss" for genome rearrangement in Crassostrea? / Bmc Genomics 2008., 9:
  50. Bernt M, Merkle D, Ramsch K, Fritzsch G, Perseke M, Bernhard D, Schlegel M, Stadler PF, Middendorf M: CREx: inferring genomic rearrangements based on common intervals. / Bioinformatics 2007,23(21):2957鈥?958. CrossRef
  51. Lavrov DV, Boore JL, Brown WM: Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: Duplication and nonrandom loss. / Molecular Biology and Evolution 2002,19(2):163鈥?69.
  52. Moritz C, Brown WM: Tandem duplication of D-loop and ribosomal RNA sequences in lizard mitochondrial DNA. / Science 1986,233(4771):1425鈥?427. CrossRef
  53. Lunt DH, Hyman BC: Animal mitochondrial DNA recombination. / Nature 1997,387(6630):247鈥?47. CrossRef
  54. Shao RF, Barker SC: The highly rearranged mitochondrial genome of the plague thrips, Thrips imaginis (Insecta: thysanoptera): Convergence of two novel gene boundaries and an extraordinary arrangement of rRNA genes. / Molecular Biology and Evolution 2003,20(3):362鈥?70. CrossRef
  55. Ladoukakis ED, Zouros E: Recombination in animal mitochondrial DNA: Evidence from published sequences. / Molecular Biology and Evolution 2001,18(11):2127鈥?131.
  56. Gibson T, Blok VC, Phillips MS, Hong G, Kumarasinghe D, Riley IT, Dowton M: The mitochondrial subgenomes of the nematode Globodera pallida are mosaics: Evidence of recombination in an animal mitochondrial genome. / Journal of Molecular Evolution 2007,64(4):463鈥?71. CrossRef
  57. Burger G, Lavrov DV, Forget L, Lang BF: Sequencing complete mitochondrial and plastid genomes. / Nature Protocols 2007,2(3):603鈥?14. CrossRef
  58. Armstrong MR, Blok VC, Phillips MS: A multipartite mitochondrial genome in the potato cyst nematode Globodera pallida. / Genetics 2000,154(1):181鈥?92.
  59. Pamilo P, Viljakainen L, Vihavainen A: Exceptionally high density of NUMTs in the honeybee genome. / Molecular Biology and Evolution 2007,24(6):1340鈥?346. CrossRef
  60. Richly E, Leister D: NUPTs in sequenced eukaryotes and their genomic organization in relation to NUMTs. / Molecular Biology and Evolution 2004,21(10):1972鈥?980. CrossRef
  61. Paabo S, Irwin DM, Wilson AC: DNA Damage Promotes Jumping between Templates during Enzymatic Amplification. / Journal of Biological Chemistry 1990,265(8):4718鈥?721.
  62. Piganeau G, Gardner M, Eyre-Walker A: A broad survey of recombination in animal mitochondria. / Molecular Biology and Evolution 2004,21(12):2319鈥?325. CrossRef
  63. Smith JM, Smith NH: Recombination in animal mitochondrial DNA. / Molecular Biology and Evolution 2002,19(12):2330鈥?332.
  64. Rota-Stabelli O, Kayal E, Gleeson D, Daub J, Boore JL, Telford MJ, Pisani D, Blaxter M, Lavrov DV: Ecdysozoan Mitogenomics: Evidence for a Common Origin of the Legged Invertebrates, the Panarthropoda. / Genome Biol Evol 2010, 2:425鈥?40. CrossRef
  65. Koenemann S, Jenner RA, Hoenemann M, Stemme T, von Reumont BM: Arthropod phylogeny revisited, with a focus on crustacean relationships. / Arthropod Struct Dev 2010,39(2鈥?):88鈥?10. CrossRef
  66. Huys R, Llewellyn-Hughes J, Conroy-Dalton S, Olson PD, Spinks JN, Johnston DA: Extraordinary host switching in siphonostomatoid copepods and the demise of the Monstrilloida: Integrating molecular data, ontogeny and antennulary morphology. / Mol Phylogenet Evol 2007,43(2):368鈥?78. CrossRef
  67. Huys R, Llewellyn-Hughes J, Olson PD, Nagasawa K: Small subunit rDNA and Bayesian inference reveal Pectenophilus ornatus (Copepoda incertae sedis) as highly transformed Mytilicolidae, and support assignment of Chondracanthidae and Xarifiidae to Lichomolgoidea (Cyclopoida). / Biol J Linn Soc 2006,87(3):403鈥?25. CrossRef
  68. Sperling EA, Peterson KJ, Pisani D: Phylogenetic-Signal Dissection of Nuclear Housekeeping Genes Supports the Paraphyly of Sponges and the Monophyly of Eumetazoa. / Molecular biology and evolution 2009,26(10):2261鈥?274. CrossRef
  69. Regier JC, Shultz JW, Zwick A, Hussey A, Ball B, Wetzer R, Martin JW, Cunningham CW: Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. / Nature 2010,463(7284):1079-U1098. CrossRef
  70. Giribet G, Edgecombe GD, Wheeler WC: Arthropod phylogeny based on eight molecular loci and morphology. / Nature 2001,413(6852):157鈥?61. CrossRef
  71. Boore JL, Lavrov DV, Brown WM: Gene translocation links insects and crustaceans. / Nature 1998,392(6677):667鈥?68. CrossRef
  72. Carapelli A, Lio P, Nardi F, van der Wath E, Frati F: Phylogenetic analysis of mitochondrial protein coding genes confirms the reciprocal paraphyly of Hexapoda and Crustacea. / BMC evolutionary biology 2007., 7:
  73. Regier JC, Shultz JW, Kambic RE: Pancrustacean phylogeny: hexapods are terrestrial crustaceans and maxillopods are not monophyletic. / Proc Biol Sci 2005,272(1561):395鈥?01. CrossRef
  74. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R: DnaSP, DNA polymorphism analyses by the coalescent and other methods. / Bioinformatics 2003,19(18):2496鈥?497. CrossRef
  75. Foltz DW: Invertebrate species with nonpelagic larvae have elevated levels of nonsynonymous substitutions and reduced nucleotide diversities. / Journal of Molecular Evolution 2003,57(6):607鈥?12. CrossRef
  76. Ewing B, Hillier L, Wendl MC, Green P: Base-calling of automated sequencer traces using phred. I. Accuracy assessment. / Genome Res 1998,8(3):175鈥?85.
  77. Ewing B, Green P: Base-calling of automated sequencer traces using phred. II. Error probabilities. / Genome Res 1998,8(3):186鈥?94.
  78. Gordon D, Abajian C, Green P: Consed: A graphical tool for sequence finishing. / Genome Res 1998,8(3):195鈥?02.
  79. Lowe TM, Eddy SR: tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. / Nucleic Acids Res 1997,25(5):955鈥?64. CrossRef
  80. Laslett D, Canback B: ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. / Bioinformatics 2008,24(2):172鈥?75. CrossRef
  81. Derijk P, Dewachter R: Dcse, an Interactive Tool for Sequence Alignment and Secondary Structure Research. / Computer Applications in the Biosciences 1993,9(6):735鈥?40.
  82. De Rijk P, Wuyts J, De Wachter R: RnaViz 2: an improved representation of RNA secondary structure. / Bioinformatics 2003,19(2):299鈥?00. CrossRef
  83. Zuker M: Mfold web server for nucleic acid folding and hybridization prediction. / Nucleic Acids Research 2003,31(13):3406鈥?415. CrossRef
  84. Yang ZH: PAML 4: Phylogenetic analysis by maximum likelihood. / Molecular Biology and Evolution 2007,24(8):1586鈥?591. CrossRef
  85. Roshan U, Livesay DR: Probalign: multiple sequence alignment using partition function posterior probabilities. / Bioinformatics 2006,22(22):2715鈥?721. CrossRef
  86. Brinkmann H, Philippe H: Archaea sister group of bacteria? Indications from tree reconstruction artefacts in ancient phylogenies. / Mol Biol Evol 1999,16(6):817鈥?25.
  
• 作者单位：Wang Minxiao (1) (2)
  Sun Song (1)
  Li Chaolun (1)
  Shen Xin (3)
  
  1. KLMEES and JBMERS, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
  2. Graduate University, Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100039, China
  3. Huaihai Institute of Technology, 59 Cangwu Road, Lianyungang, 222005, China
  

文摘

Background Copepods are highly diverse and abundant, resulting in extensive ecological radiation in marine ecosystems. Calanus sinicus dominates continental shelf waters in the northwest Pacific Ocean and plays an important role in the local ecosystem by linking primary production to higher trophic levels. A lack of effective molecular markers has hindered phylogenetic and population genetic studies concerning copepods. As they are genome-level informative, mitochondrial DNA sequences can be used as markers for population genetic studies and phylogenetic studies. Results The mitochondrial genome of C. sinicus is distinct from other arthropods owing to the concurrence of multiple non-coding regions and a reshuffled gene arrangement. Further particularities in the mitogenome of C. sinicus include low A + T-content, symmetrical nucleotide composition between strands, abbreviated stop codons for several PCGs and extended lengths of the genes atp6 and atp8 relative to other copepods. The monophyletic Copepoda should be placed within the Vericrustacea. The close affinity between Cyclopoida and Poecilostomatoida suggests reassigning the latter as subordinate to the former. Monophyly of Maxillopoda is rejected. Within the alignment of 11 C. sinicus mitogenomes, there are 397 variable sites harbouring three 'hotspot' variable sites and three microsatellite loci. Conclusion The occurrence of the circular subgenomic fragment during laboratory assays suggests that special caution should be taken when sequencing mitogenomes using long PCR. Such a phenomenon may provide additional evidence of mitochondrial DNA recombination, which appears to have been a prerequisite for shaping the present mitochondrial profile of C. sinicus during its evolution. The lack of synapomorphic gene arrangements among copepods has cast doubt on the utility of gene order as a useful molecular marker for deep phylogenetic analysis. However, mitochondrial genomic sequences have been valuable markers for resolving phylogenetic issues concerning copepods. The variable site maps of C. sinicus mitogenomes provide a solid foundation for population genetic studies.