The mitochondrial genome of the onychophoran Opisthopatus cinctipes (Peripatopsidae) reflects the ancestral mitochondrial gene arrangement of Panarthropoda and Ecdysozoa

Molecular Phylogenetics and Evolution

Volumn 57, Issue 1, 2010, Pages 285-292

  Braband, Anke ^a   Cameron, Stephen L ^b   Podsiadlowski, Lars ^c   Daniels, Savel R ^d   Mayer, Georg ^e  

^a HUMBOLDT UNIVERSITY   (Germany)

^b CSIRO   (Australia)

^c UNIVERSITY OF BONN   (Germany)

^d STELLENBOSCH UNIVERSITY   (South Africa)

^e UNIVERSITY OF LEIPZIG   (Germany)

Author keywords

Arthropods; Gene order; Onychophora; Phylogeny; Velvet worms

Indexed keywords

ANIMAL; ARTHROPOD; ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; DNA SEQUENCE; GENE ORDER; GENETICS; INVERTEBRATE; MITOCHONDRIAL GENOME; PHYLOGENY;

ANIMALS; ARTHROPODS; COMPARATIVE GENOMIC HYBRIDIZATION; GENE ORDER; GENOME, MITOCHONDRIAL; INVERTEBRATES; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

ARTHROPODA; ECDYSOZOA; EPIPERIPATUS BIOLLEYI; ONYCHOPHORA; OPISTHOPATUS CINCTIPES; PANARTHROPODA; PERIPATIDAE; PERIPATOPSIDAE; PRIAPULIDA; PROTOSTOMIA;

EID: 77956231198     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2010.05.011     Document Type: Article

References (51)

1. Ballard J.W.O., Olsen G.J., Faith D.P., Odgers W.A., Rowell D.M., Atkinson P.W. Evidence from 12S ribosomal RNA sequences that onychophorans are modified arthropods. Science 1992, 258:1345-1348.
2. Blanchette M., Kunisawa T., Sankoff D. Gene order breakpoint evidence in animal mitochondrial phylogeny. J. Mol. Evol. 1999, 49:193-203.
3. Bleidorn C., Eeckhaut I., Podsiadlowski L., Schult N., McHugh D., Halanych K.M., Milinkovitch M.C., Tiedemann R. Mitochondrial genome and nuclear sequence data support Myzostomida as part of the annelid radiation. Mol. Biol. Evol. 2007, 24:1690-1701.
4. Boore J.L. Animal mitochondrial genomes. Nucleic Acids Res. 1999, 27:1767-1780.
5. Boore J.L., Collins T.M., Stanton D., Daehler L.L., Brown W.M. Deducing the pattern of arthropod phylogeny from mitochondrial DNA rearrangements. Nature 1995, 376:163-165.
6. Boore J.L., Lavrov D.V., Brown W.M. Gene translocation links insects and crustaceans. Nature 1998, 392:667-668.
7. Braband A., Podsiadlowski L., Cameron S.L., Daniels S., Mayer G. Extensive duplication events account for multiple control regions and pseudogenes in the mitochondrial genome of the velvet worm Metaperipatus inae (Onychophora, Peripatopsidae). Mol. Phylogenet. Evol. 2010, 57:293-300.
8. Cameron S.L., Barker S.C., Whiting M.F. Mitochondrial genomics and the new insect order Mantophasmatodea. Mol. Phylogenet. Evol. 2006, 38:274-279.
9. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 2000, 17:540-552.
10. Clary D.O., Wolstenholme D.R. The mitochondrial DNA molecule of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code. J. Mol. Evol. 1985, 22:252-271.
11. Dowton M., Castro L.R., Austin A.D. Mitochondrial gene rearrangements as phylogenetic characters in the invertebrates: the examination of genome 'morphology'. Invertebr. Syst. 2002, 16:345-356.
12. Dunn C.W., Hejnol A., Matus D.Q., Pang K., Browne W.E., Smith S.A., Seaver E., Rouse G.W., Obst M., Edgecombe G.D., Sørensen M.V., Haddock S.H.D., Schmidt-Rhaesa A., Okusu A., Kristensen R.M., Wheeler W.C., Martindale M.Q., Giribet G. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 2008, 452:745-749.
13. Edgecombe G.D. Palaeontological and molecular evidence linking arthropods, onychophorans, and other Ecdysozoa. Evol. Edu. Outreach 2009, 2:178-190.
14. Fahrein K., Talarico G., Braband A., Podsiadlowski L. The complete mitochondrial genome of Pseudocellus pearsei (Chelicerata: Ricinulei) and a comparison of mitochondrial gene rearrangements in Arachnida. BMC Genomics 2007, 8:386.
15. Fenn J.D., Song H., Cameron S.L., Whiting M.F. A preliminary mitochondrial genome phylogeny of Orthoptera (Insecta) and approaches to maximizing phylogenetic signal found within mitochondrial genome data. Mol. Phylogenet. Evol. 2008, 49:49-68.
16. Folmer O., Black M., Hoeh W., Lutz R., Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 1994, 3:294-299.
17. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 1999, 41:95-98.
18. 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, 38:100-116.
19. 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. Syst. Biol. 2005, 54:277-298.
20. Hejnol, A., Obst, M., Stamatakis, A., Ott, M., Rouse, G.W., Edgecombe, G.D., Martinez, P., Baguñà, J., Bailly, X., Jondelius, U., Wiens, M., Müller, W.E.G., Seaver, E., Wheeler, W.C., Martindale, M.Q., Giribet, G., Dunn, C.W., 2009. Assessing the root of bilaterian animals with scalable phylogenomic methods. Proc. R. Soc. B. doi:10.1098/rspb.2009.0896.
21. Jobb G., von Haeseler A., Strimmer K. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol. Biol. 2004, 4:18.
22. Jones M., Gantenbein B., Fet V., Blaxter M. The effect of model choice on phylogenetic inference using mitochondrial sequence data: lessons from the scorpions. Mol. Phylogenet. Evol. 2007, 43:583-595.
23. 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, 7:241.
24. Kocher T.D., Thomas W.K., Meyer A., Edwards S.V., Paabo S., Villablanca F.X., Wilson A.C. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing of conserved primers. Proc. Natl. Acad. Sci. USA 1989, 86:6196-6200.
25. Kusche K., Ruhberg H., Burmester T. A hemocyanin from the Onychophora and the emergence of respiratory proteins. Proc. Natl. Acad. Sci. USA 2002, 99:10545-10548.
26. Laslett D., Canbäck B. ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 2008, 24:172-175.
27. Lavrov D.V., Brown W.M. Trichinella spiralis mtDNA: a nematode mitochondrial genome that encodes a putative ATP8 and normally structured tRNAs and has a gene arrangement relatable to those of coelomate metazoans. Genetics 2001, 157:621-637.
28. Lowe T.M., Eddy S.R. TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997, 25:955-964.
29. Mallatt J., Giribet G. Further use of nearly complete 28S and 18S rRNA genes to classify Ecdysozoa: 37 more arthropods and a kinorhynch. Mol. Biol. Evol. 2006, 40:772-794.
30. Mayer G., Whitington P.M. Neural development in Onychophora (velvet worms) suggests a step-wise evolution of segmentation in the nervous system of Panarthropoda. Dev. Biol. 2009, 335:263-275.
31. Mayer G., Whitington P.M. Velvet worm development links myriapods with chelicerates. Proc. R. Soc. B 2009, 276:3571-3579.
32. Moritz C., Dowling T.E., Brown W.M. Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Annu. Rev. Ecol. Syst. 1987, 18:269-292.
33. 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, 10:27.
34. Nielsen C. Animal evolution: interrelationships of the Living Phyla 2001, Oxford University Press, Oxford.
35. Perna N.T., Kocher T.D. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J. Mol. Evol. 1995, 41:353-358.
36. Pie M.R., Oliveira-Neto J.F., Boeger W.A., Ostrensky A., Baggio R.A. The organization of the mitochondrial control region in 2 brachyuran crustaceans: Ucides cordatus (Ocypodidae) and Cardisoma guanhumi (Gecarcinidae). J. Heredity 2008, 99:432-437.
37. Podsiadlowski L., Braband A., Mayer G. 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.
38. Richter S. The Tetraconata concept: hexapod-crustacean relationships and the phylogeny of Crustacea. Org. Divers. Evol. 2002, 2:217-237.
39. Roeding F., Hagner-Holler S., Ruhberg H., Ebersberger I., von Haeseler A., Kube M., Reinhardt R., Burmester T. EST sequencing of Onychophora and phylogenomic analysis of Metazoa. Mol. Phylogenet. Evol. 2007, 45:942-951.
40. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
41. Rota-Stabelli O., Telford M.J. A multi criterion approach for the selection of optimal outgroups in phylogeny: recovering some support for Mandibulata over Myriochelata using mitogenomics. Mol. Phylogenet. Evol. 2008, 48:103-111.
42. Ryu S.H., Lee J.M., Jang K.-H., Choi E.H., Park S.J., Chang C.Y., Kim W., Hwang U.W. Partial mitochondrial gene arrangements support a close relationship between Tardigrada and Arthropoda. Mol. Cells 2007, 24:351-357.
43. Saccone C., De G.C., Gissi C., Pesole G., Reyes A. Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system. Gene 1999, 238:195-209.
44. Saccone C., Gissi C., Reyes A., Larizza A., Sbisa E., Pesole G. Mitochondrial DNA in Metazoa: degree of freedom in a frozen event. Gene 2002, 286:3-12.
45. Schmidt-Rhaesa A., Bartolomaeus T., Lemburg C., Ehlers U., Garey J.R. The position of the Arthropoda in the phylogenetic system. J. Morphol. 1998, 238:263-285.
46. Staton J.L., Daehler L.L., Brown W.M. Mitochondrial gene arrangement of the horseshoe crab Limulus polyphemus L.: conservation of major features among arthropod classes. Mol. Biol. Evol. 1997, 14:867-874.
47. Strausfeld N.J., Strausfeld C.M., Loesel R., Rowell D., Stowe S. Arthropod phylogeny: onychophoran brain organization suggests an archaic relationship with a chelicerate stem lineage. Proc. R. Soc. B 2006, 273:1857-1866.
48. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22:4673-4680.
49. Valverde J.R., Batuecas B., Moratilla C., Marco R., Garesse R. The complete mitochondrial DNA sequence of the crustacean Artemia franciscana. J. Mol. Evol. 1994, 39:400-408.
50. Webster B.L., Copley R.R., Jenner R.A., Mackenzie-Dodds J.A., Bourlat S.J., Rota-Stabelli O., Littlewood D.T.J., Telford M.J. Mitogenomics and phylogenomics reveal priapulid worms as extant models of the ancestral Ecdysozoan. Evol. Dev. 2006, 8:502-510.
51. Webster B.L., Mackenzie-Dodds J.A., Telford M.J., Littlewood D.T.J. The mitochondrial genome of Priapulus caudatus Lamarck (Priapulida: Priapulidae). Gene 2007, 389:96-105.