Complete mitochondrial genome of Bugula neritina (Bryozoa, Gymnolaemata, Cheilostomata): Phylogenetic position of Bryozoa and phylogeny of lophophorates within the Lophotrochozoa

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Jang, Kuem Hee ^a   Hwang, Ui Wook ^a  

^a Kyungpook National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSFER RNA; RIBOSOME RNA;

ARTICLE; BRYOZOA; BUGULA NERITINA; CONTROLLED STUDY; GENE CLUSTER; GENE LOCATION; GENE LOSS; GENE REARRANGEMENT; GENE STRUCTURE; GENOME ANALYSIS; LOPHOTROCHOZOA; METAZOON; MITOCHONDRIAL GENOME; MITOCHONDRION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE HOMOLOGY; SPECIES COMPARISON; TAXONOMY; ANIMAL; CHEMISTRY; CLASSIFICATION; CODON; CONFORMATION; GENETICS; INVERTEBRATE; METABOLISM; MOLECULAR GENETICS;

ANNELIDA; BRACHIOPODA; BRYOZOA; BUGULA NERITINA; CHEILOSTOMATIDA; CTENOSTOMATA; ECHIURA; ENTOPROCTA; FLUSTRELLIDRA HISPIDA; GYMNOLAEMATA; KATHARINA; LOPHOTROCHOZOA; METAZOA; PHORONIFORMEA;

ANIMALS; BRYOZOA; CODON; GENOME, MITOCHONDRIAL; INVERTEBRATES; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; RNA, RIBOSOMAL; RNA, TRANSFER;

EID: 65549164448     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-167     Document Type: Article

References (67)

1. McKinney ML Jackson JBC Bryozoan Evolution Chicago: University of Chicago Press 1989.
2. Hayward PJ Ryland JS Cheilostomatous Bryozoa Part 1 Aeteoidea-Cribrilinoidea Brill and Backhuys Hayward PJ, Ryland JS 1998.
3. Ryland JS Bryozoa: An introductory overview Moostiere (Bryozoa), Moss Animals (Bryozoa) Denisia Wöss ER 2005, 16:9-20.
4. Hyman LH The invertebrates: Smaller coelomate groups New York; Toronto; London: McGraw-Hill 1959.
5. Emig CC On the origin of the lophophorata Z Zool Syst Evolut-Forsch 1984, 22:91-94.
6. Brusca RC Brusca GJ Invertebrates Sunderland, MA: Sinauer Associates Inc 1990.
7. Willmer P Invertebrate Relationships: Patterns in animal evolution New York: Cambrige University Press 1990.
8. Eming CC Les lophophorates constituent-ils un embranchement? Bull Soc Zool France 1997, 122:279-288.
9. Eernisse DJ Albert JS FE A Annelida and arthropoda are not sister taxa: a phylogenetic analysis of spiralian metazoan phylogeny Syst Biol 1992, 41:305-330.
10. Nielsen C Scharff N Eibye-Jacobsen D Cladistic analyses of the animal kingdom Biol J Linn Soc Lond 1996, 57:385-410. 10.1111/ j.1095-8312.1996.tb01857.x
11. Zrzavy J Milhulka S Kepka P Bezdek A Tietz DF Phylogeny of the Metazoa based on morphological and 18S ribosomal DNA evidence Cladistics 1998, 14:249-285.
12. Nielsen C Animal evolution: Interrelationships of the living phyla USA, Oxford University Press Nielsen C 2 2001:232-263.
13. Brusca RC Brusca GJ Invertebrates MA, Sinauer Press Brusca RC, Brusca GJ 2 2003:771-779.
14. Conway-Morris S Nailing the Lophophorates Science 1995, 375:365-366.
15. Halanych KM Bacheller JD Aguinaldo AM Liva SM Hillis DM Lake JA Evidence from 18S ribosomal DNA that the lophophorates are protostome animals Science 1995, 267:1641-1643. 10.1126/science.7886451 7886451
16. Conway-Morris S Cohen BL Gawthrop AB Cavalier-Smith T Winnepenninckx B Lophophorate phylogeny Science 1996, 272:282. 10.1126/ science.272.5259.282 8602516
17. Mackey LY Winnepenninckx B Dewachter R Backeljau T Emschermann P Garey JR 18S rRNA suggests that Entoprocta are protostomes, unrelated to Ectoprocta J Mol Evol 1996, 42:552-559. 10.1007/BF02352285 8662007
18. Cohen BL Gawthrop AB The brachiopod genome Treatise on invertebrate paleontology Geological Society of America and University of Kansas Press Williams A, Lawrence KS 1997:189-211.
19. Giribet G Distel DL Polz M Sterrer W Wheeler WC Triploblastic relationships with emphasis on the acoelomates and the position of Gnathostomulida, Cycliophora, Platyhelminthes, and Chaetognatha: A combined approach of 18S rDNA sequences an morphology Syst Biol 2000, 49:539-562. 10.1080/10635159950127385 12116426
20. Passamaneck YL Halanych KM Evidence from Hox genes that bryozoans are lophotrochozoans Evol Develop 2004, 6:275-281. 10.1111/ j.1525-142X.2004.04032.x
21. Peterson KJ Eernisse DJ Animal phylogeny and the ancestry of bilaterians: Inferences from morphology and 18S rDNA gene sequences Evol Develop 2001, 3:170-205. 10.1046/j.1525-142x.2001.003003170.x
22. Field KG Olsen GJ Lane DJ Giovannoni SJ Ghiselin MT Raff EC Pace MR Raff RA Molecular phylogeny of the animal kingdom Science 1988, 239:748-753. 10.1126/science.3277277 3277277
23. Cohen BL Gawthrop AB Cavalier-Smith T Molecular phylogeny of brachiopods and phoronids based on nuclear-encoded small subunit ribosomal RNA gene sequences Phil Trans R Soc Lond B 1998, 353:2039-2061. 10.1098/ rstb.1998.0351
24. Cohen BL Stark S Gawthrop AB Burke ME Thayer CW Comparison of articulate brachiopod nuclear and mitochondrial gene trees leads to a clade-based redefinition of protostomes Protostomozoa and deuterostomes Deuterostomozoa Proc R Soc Lond Ser B Biol Sci 1998, 265:475-482. 10.1098/rspb.1998.0319
25. Wolstenholme DR Animal mitochondrial DNA: Structure and evolution Int Rev Cytol 1992, 141:173-216. 10.1016/S0074-7696(08)62066-5 1452431
26. Hassanin A Léger 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 Syst Biol 2005, 54:277-298. 10.1080/10635150590947843 16021696
27. Swire J Judson O Burt A Mitochondrial genetic codes evolve to match amino acid requirements of proteins J Mol Evol 2005, 60:128-139. 10.1007/ s00239-004-0077-9 15696375
28. Stechmann A Schlegel M Analysis of the complete mitochondrial DNA sequence of the brachiopod Tereburatulina retusa places Brachiopoda within the protosmes P Roy Soc B Biol Sci 1999, 266:2043-2052. 10.1098/ rspb.1999.0885
29. Helfenbein KG Boore JL The mitochondrial genome of Phoronis architecta comparisons demonstrate that phoronids are lophotrochozoan protosmes Mol Biol Evol 2004, 21:153-157. 10.1093/molbev/msh011 14595093
30. Cavalier-Smith T A revised six-kingdom system of life Biol Rev 1998, 73:203-266. 10.1017/S0006323198005167 9809012
31. Waeschenbach A Telford MJ Porter JS Littlewood TJ The complete mitochondrial genome of Flustrellidra hispida and the phylogenetic position of Bryozoa among the Metazoa Mol Phylogenet Evol 2006, 40:195-207. 10.1016/j.ympev.2006.03.007 16621614
32. Clayton DA Replication of animal mitochondrial DNA Cell 1982, 28:693-705. 10.1016/0092-8674(82)90049-6 6178513
33. Clayton DA Replication and transcription of vertebrate mitochondrial DNA Annu Rev Cell Biol 1999, 7:453-478. 10.1146/annurev.cb.07.110191.002321
34. Jacobs HT Elliott DJ Math VB Farquharson A Nucleotide sequence and gene organization of sea urchin mitochondrial DNA J Mol Biol 1988, 202:185-217. 10.1016/0022-2836(88)90452-4 3172215
35. Tomita K Yokobori SI Oshima T Ueda T Watanabae K The Cephalopod Loligo bleekeri mitochondrial genome: Multipled noncoding regions and transposition of tRNA genes J Mol Biol 2002, 54:486-500.
36. Serb JM Lydeard C Complete mtDNA sequence of the North American freshwater mussel, Lampsilis ornata (Unionidae): An examination of the evolution and phylogenetic utility of mitochondrial genome organization in bivalvia (Molluska) Mol Biol Evol 2003, 20:1854-1866. 10.1093/molbev/ msg218 12949150
37. Noguchi Y Endo K Tajima F Ueshima R The mitochondrial genome of the brachiopod Laqueus rubellus Genetics 2000, 155:245-259. 1461069 10790399
38. Boore JL Brown WM Complete sequence of the mitocondrial DNA of the annelid worm Lumburicus terrestris Genetics 1995, 141:305-319. 1206728 8536978
39. Wolstenholme DR Okimoto R Macfarlane JL Nucleotide correlations that suggest tertiary interactions in the TV-replacement loop-containing tochondrial tRNAs of the nematodes, Caenorhabditis elegans and Ascaris suum Nucleic Acids Res 1994, 22:4300-4306. 331950 7937159 10.1093/nar/ 22.20.4300
40. Boore JL Brown WM Complete DNA sequence of the mitochondrial genome of the black chiton, Katharina tunicate Genetics 1994, 138:423-443. 1206160 7828825
41. Yamazaki N Ueshima R Terrett JA Thomas RH Evolution of pulmonate gastropod mitochondrial genomes: Comparisons of gene organizations of Euhadra, Cepaea and Albinaria and implications of unusual tRNA secondary structures Genetics 1997, 145:749-758. 1207859 9055084
42. Helfenbein KG Brown WM Boore JL The complete mitochondrial genome of the articulate brachiopoda Terabratalia transversa Mol Biol Evol 2001, 18:1734-1744. 11504853
43. Jeyaprakash A Hoy M The mitochondrial genome of the predatory mite Metaseiulus occidentalis (Arthropoda: Chelicerata: Acari: Phytoseiidae) is unexpectedly large and contains several novel features Gene 2007, 391:264-274. 10.1016/j.gene.2007.01.012 17321074
44. Lars P Anke B Georg M The complete mitochondrial genome of the Onychophoran Epiperipatus biolleyi reveals a unique transfer RNA set and provides further support for the ecdysozoa hypothesis Mol Biol Evol 2008, 25:42-51. 17934206
45. Yokobori S Iseto T Asakawa S Sasaki T Shimizu N Yamagishi A Oshima T Hirose E Complete nucleotide sequences of mitochondrial genomes of two solitary entoprocts, Loxocorone allax and Loxosomella aloxiata: Implications for ophotrochozoan phylogeny Mol Phylogenet Evol 2008, 47(2):612-628. 10.1016/j.ympev.2008.02.013 18374604
46. Eernisse DJ Arthropod and annelid relationships re-examined London: Chapman & Hall 1997
47. Anderson FE Córdoba AJ Thollesson M Bilaterian phylogeny based on analyses of a region of the sodium-potassium ATPase α-subunit gene J Mol Evol 2004, 58:252-268. 10.1007/s00239-003-2548-9 15045481
48. Cohen BL Monophyly of brachiopods and phoronids: Reconciliation of molecular evidence with Linnaean classification (the subphylum Phoronifirmea nov.) Proc R Soc Lond B 2000, 267:225-231. 10.1098/ rspb.2000.0991
49. Dunn C Hejnol a Matus D Pang K Browne W Smith S Seaver E Rouse G Obst M Edgecombe G et al Broad phylogenomic sampling improves resolution of the animal tree of life Nature 2008, 452:745-749. 10.1038/nature06614 18322464
50. Hausdorf B Helmkampf M Meyer A Witek A Herlyn H Bruchhaus I Hankeln T Struck T Lieb B Spiralian Phylogenomics Supports the Resurrection of Bryozoa Comprising Ectoprocta and Entoprocta Mol Biol Evol 2007, 24:2723-2729. 10.1093/molbev/msm214 17921486
51. Helmkampf M Bruchhaus I Hausdorf B Phylogenomic analyses of lophophorates (brachiopods, phoronids and bryozoans) confirm the Lophotrochozoa concept Proc R Soc B 2008, 275:1927-1933. 10.1098/ rspb.2008.0372 18495619
52. Adoutte A Balavoine G Lartillot N Lespinet O Prud'homme B De Rosa R The new animal phylogeny: Reliability and implications Proc Natl Acad Sci U S A 2000, 97(9):4453-4456. 34321 10781043 10.1073/pnas.97.9.4453
53. Halanych K The new view of animal phylogeny Ann Rev Ecol Evol Syst 2004, 35:229-256. 10.1146/annurev.ecolsys.35.112202.130124
54. Simon C Frati F Beckenbach A Crespi B Liu H Flook P Evolution, weighting and phylogenetic utility of mitochondrial gene sequences and a comilation of conserved polymerase chain reaction primers Ann Entomol Soc Amer 1994, 87:651-701.
55. Folmer O Black M Hoeh R Lutz RA Vrijenhoek R DNA primers for amplification of mitochondrial cytchrome C oxidase subunit I from diverse metazoan invertebrates Mol Mar Biol Biotechnol 1994, 3:294-299. 7881515
56. Ojala D Montoya J Attardi G tRNA punctuation model of RNA processing in human mitochondria Nature 1981, 290:470-474. 10.1038/290470a0 7219536
57. Lowe TM Eddy SR tRNA-SE: A program for improved detection of transfer RNA genes in genomic sequence Nucleic Acids Res 1997, 25:955-964. 146525 9023104 10.1093/nar/25.5.955
58. Kumazawa Y Nishida M Variations in mitochondrial tRNA gene organization of reptiles as phylogenetic markers Mol Biol Evol 1995, 12:759-772. 7476123
59. Thompson JD Gibson TJ Plewniak F Jeanmougin F Higgins DG The Clustal X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 1997, 24:4876-4882. 10.1093/nar/25.24.4876
60. Castresana J Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis Mol Biol Evol 2000, 17:540-552. 10742046
61. Posada D Buckley T Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests Syst Biol 2004, 53:793-808. 10.1080/ 10635150490522304 15545256
62. Adachi J Hasegawa M Model of amino acid substitution in proteins encoded by mitochondrial DNA J Mol Evol 1996, 42:459-468. 10.1007/BF02498640 8642615
63. Posada D Crandall KA Modeltest: Testing the model of DNA substitution Bioinformaitcs 1998, 14:817-818. 10.1093/bioinformatics/14.9.817
64. Guindon S Gascuel O A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst Biol 2003, 52:696-704. 10.1080/10635150390235520 14530136
65. Jobb G TREEFINDER version of may 2006 Munich, Germany: Distributed by the author http://www.treefinder.de
66. Huelsenbeck JP Ronquist F MRBAYES: Bayesian inference of phylogenetic trees Bioinformatics 2001, 17:754-755. 10.1093/bioinformatics/17.8.754 11524383
67. Strimmer k Rambaut A Inferring confidence sets of possibly misspecified gene trees Proc R Soc B 2002, 269:137-142. 1690879 11798428 10.1098/ rspb.2001.1862