Multiple rearrangements in mitochondrial genomes of Isopoda and phylogenetic implications

Molecular Phylogenetics and Evolution

Volumn 64, Issue 1, 2012, Pages 106-117

  Kilpert, Fabian ^a   Held, Christoph ^b   Podsiadlowski, Lars ^a  

^a UNIVERSITY OF BONN   (Germany)

^b ALFRED WEGENER INSTITUTE FOR POLAR AND MARINE RESEARCH   (Germany)

Author keywords

Gene rearrangement; Isopoda; Mitochondrial genome; Phylogeny

Indexed keywords

PRIMER DNA;

ANIMAL; ANTARCTICA; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CLASSIFICATION; DNA SEQUENCE; FRANCE; GENE ORDER; GENE REARRANGEMENT; GENETICS; GERMANY; ISOPODA; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY;

ANIMALS; ANTARCTIC REGIONS; BASE SEQUENCE; BAYES THEOREM; DNA PRIMERS; EVOLUTION, MOLECULAR; FRANCE; GENE ORDER; GENE REARRANGEMENT; GENOME, MITOCHONDRIAL; GERMANY; ISOPODA; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

CRUSTACEA; ISOPODA; JANIRA; JANIRA MACULOSA; VALVIFERA;

EID: 84860592190     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2012.03.013     Document Type: Article

References (62)

1. Abascal F., Posada D., Zardoya R. MtArt: a new model of amino acid replacement for Arthropoda. Mol. Biol. Evol. 2007, 24:1-5.
2. Anderson S., Bankier A.T., Barrell B.G., de Bruijn M.H., Coulson A.R., Drouin J., Eperon I.C., Nierlich D.P., Roe B.A., Sanger F., Schreier P.H., Smith A.J., Staden R., Young I.G. Sequence and organization of the human mitochondrial genome. Nature 1981, 290:457-465.
3. Bauza-Ribot M.M., Jaume D., Juan C., Pons J. The complete mitochondrial genome of the subterranean crustacean Metacrangonyx longipes (Amphipoda): a unique gene order and extremely short control region. Mitoch. DNA 2009, 20:88-99.
4. Bogenhagen D.F., Clayton D.A. The mitochondrial DNA replication bubble has not burst. Trends Biochem. Sci. 2003, 28:357-360.
5. Boore J.L. Animal mitochondrial genomes. Nucleic Acids Res. 1999, 27:1767-1780.
6. Boore J.L., Brown W.M. Complete DNA sequence of the mitochondrial genome of the black chiton, Katharina tunicata. Genetics 1994, 138:423-443.
7. Boore J.L., Collins T.M., Stanton D., Daehler L.L., Brown W.M. Deducing the pattern of arthropod phylogeny from mitochondrial DNA rearrangements. Nat. London 1995, 376:163-165.
8. Boore J.L., Lavrov D.V., Brown W.M. Gene translocation links insects and crustaceans. Nature 1998, 392:667-668.
9. Brennicke A., Marchfelder A., Binder S. RNA editing. FEMS Microbiol. Rev. 1999, 23:297-316.
10. Brusca R.C., Wilson G.D.F. A phylogenetic analysis of the Isopoda with some classificatory recommendations. Mem. Queensland Mus. 1991, 31:143-204.
11. Clayton D.A. Replication of animal mitochondrial DNA. Cell 1982, 28:693-705.
12. Cook C.E., Yue Q., Akam M. Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic. Proc. Biol. Sci. 2005, 272:1295-1304.
13. Crozier R.H., Crozier Y.C. The mitochondrial genome of the honeybee Apis mellifera: complete sequence and genome organization. Genetics 1993, 133:97-117.
14. Cunha R.L., Grande C., Zardoya R. Neogastropod phylogenetic relationships based on entire mitochondrial genomes. BMC Evol. Biol. 2009, 9:210.
15. 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.
16. Dreyer H., Waegele J.W. The Scutocoxifera tax. nov. and the information content of nuclear ssu rDNA sequences for reconstruction of isopod phylogeny (Peracarida: Isopoda). J. Crust. Biol. 2002, 22:217-234.
17. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32:1792-1797.
18. Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 1978, 27:401-410.
19. Fernandez-Silva P., Enriquez J.A., Montoya J. Replication and transcription of mammalian mitochondrial DNA. Exp. Physiol. 2003, 88:41-56.
20. 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.
21. Gai Y., Song D., Sun H., Yang Q., Zhou K. The complete mitochondrial genome of Symphylella sp. (Myriapoda: Symphyla): extensive gene order rearrangement and evidence in favor of Progoneata. Mol. Phylogenet. Evol. 2008, 49:574-585.
22. Gissi C., Iannelli F., Pesole G. Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species. Heredity 2008, 101:301-320.
23. Grande C., Templado J., Zardoya R. Evolution of gastropod mitochondrial genome arrangements. BMC Evol. Biol. 2008, 8:61.
24. Haen K.M., Lang B.F., Pomponi S.A., Lavrov D.V. Glass sponges and bilaterian animals share derived mitochondrial genomic features: a common ancestry or parallel evolution?. Mol. Biol. Evol. 2007, 24:1518-1527.
25. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids. Symp. Ser. 1999, 41:95-98.
26. 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.
27. 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.
28. Ito A., Aoki M.N., Yokobori S., Wada H. The complete mitochondrial genome of Caprella scaura (Crustacea, Amphipoda, Caprellidea), with emphasis on the unique gene order pattern and duplicated control region. Mitoch. DNA 2010, 21:183-190.
29. Jobb G., von Haeseler A., Strimmer K. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol. Biol. 2004, 4:18.
30. Ki J.S., Park H.G., Lee J.S. The complete mitochondrial genome of the cyclopoid copepod Paracyclopina nana: a highly divergent genome with novel gene order and atypical gene numbers. Gene 2009, 435:13-22.
31. Ki J.S., Hop H., Kim S.J., Kim I.C., Park H.G., Lee J.S. Complete mitochondrial genome sequence of the Arctic gammarid, Onisimus nanseni (Crustacea; Amphipoda): Novel gene structures and unusual control region features. Comp. Biochem. Physiol. D 2010, 5:105-115.
32. 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.
33. Kilpert F., Podsiadlowski L. The Australian fresh water isopod (Phreatoicidea: Isopoda) allows insights into the early mitogenomic evolution of isopods. Comp. Biochem. Phys. D 2009, 5:36-44.
34. Kilpert F., Podsiadlowski L. The mitochondrial genome of the Japanese skeleton shrimp Caprella mutica (Amphipoda: Caprellidea) reveals a unique gene order and shared apomorphic translocations with Gammaridea. Mitoch. DNA 2010, 21:77-86.
35. Laslett D., Canback B. ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 2008, 24:172-175.
36. Lavrov D.V., Brown W.M., Boore J.L. Phylogenetic position of the Pentastomida and (pan)crustacean relationships. Proc. Roy. Soc. Lond. B Biol. Sci. 2004, 271:537-544.
37. Liu Y., Cui Z. Complete mitochondrial genome of the Asian paddle crab Charybdis japonica (Crustacea: Decapoda: Portunidae): gene rearrangement of the marine brachyurans and phylogenetic considerations of the decapods. Mol. Biol. Rep. 2009, 37:2559-2569.
38. 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.
39. Marcade I., Cordaux R., Doublet V., Debenest C., Bouchon D., Raimond R. Structure and evolution of the atypical mitochondrial genome of Armadillidium vulgare (Isopoda, Crustacea). J. Mol. Evol. 2007, 65:651-659.
40. Mindell D.P., Sorenson M.D., Dimcheff D.E. Multiple independent origins of mitochondrial gene order in birds. Proc. Natl. Acad. Sci. USA 1998, 95:10693-10697.
41. Ojala D., Montoya J., Attardi G. TRNA punctuation model of RNA processing in human mitochondria. Nature 1981, 290:470-474.
42. Oliveira D.C., Raychoudhury R., Lavrov D.V., Werren J.H. Rapidly evolving mitochondrial genome and directional selection in mitochondrial genes in the parasitic wasp Nasonia (Hymenoptera: Pteromalidae). Mol. Biol. Evol. 2008, 25:2167-2180.
43. Pisani D., Poling L.L., Lyons-Weiler M., Hedges S.B. The colonization of land by animals: molecular phylogeny and divergence times among arthropods. BMC Biol. 2004, 2:1.
44. Podsiadlowski L., Bartolomaeus T. Organization of the mitochondrial genome of mantis shrimp Pseudosquilla ciliata (Crustacea: Stomatopoda). Mar. Biotechnol. 2005, 7:618-624.
45. Podsiadlowski L., Bartolomaeus T. Major rearrangements characterize the mitochondrial genome of the isopod Idotea baltica (Crustacea: Peracarida). Mol. Phylogenet. Evol. 2006, 40:893-899.
46. Raimond R., Marcade I., Bouchon D., Rigaud T., Bossy J.P., Souty-Grosset C. Organization of the large mitochondrial genome in the isopod Armadillidium vulgare. Genetics 1999, 151:203-210.
47. Rawlings T.A., Collins T.M., Bieler R. Changing identities: tRNA duplication and remolding within animal mitochondrial genomes. Proc. Natl. Acad. Sci. USA 2003, 100:15700-15705.
48. Roehrdanz R.L., Degrugillier M.E., Black W.C.I. Novel rearrangements of arthropod mitochondrial DNA detected with long-PCR: applications to arthropod phylogeny and evolution. Mol. Biol. Evol. 2002, 19:841-849.
49. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
50. Schmidt C. Phylogeny of the Terrestrial Isopoda (Oniscidea): a review. Arthr. Syst. Phyl. 2008, 66:191-226.
51. Schram F.R. Isopod from Pennsylvanian of Illinois. Science 1970, 169:854-855.
52. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690.
53. Stuart K.D., Schnaufer A., Ernst N.L., Panigrahi A.K. Complex management: RNA editing in trypanosomes. Trends Biochem. Sci. 2005, 30:97-105.
54. Valverde J.R., Marco R., Garesse R. A conserved heptamer motif for ribosomal RNA transcription termination in animal mitochondria. Proc. Natl. Acad. Sci. USA 1994, 91:5368-5371.
55. Wägele J.W. Evolution und phylogenetisches System der Isopoda. Zoologica 1989, 140:1-262.
56. Wilson G.D.F. Some of the deep-sea fauna is ancient. Crustaceana 1999, 72:1019-1030.
57. Wilson G.D.F. The phylogenetic position of the Isopoda in the Peracarida (Crustacea: Malacostraca). Arthr. Syst. Phyl. 2009, 67:159-198.
58. Wilson K., Cahill V., Ballment E., Benzie J. The complete sequence of the mitochondrial genome of the crustacean Penaeus monodon: are malacostracan crustaceans more closely related to insects than to branchiopods?. Mol. Biol. Evol. 2000, 17:863-874.
59. Wolstenholme D.R. Animal mitochondrial DNA: structure and evolution. Int. Rev. Cytol. 1992, 141:173-216.
60. Wu X., Xu X., Yu Z., Kong X. Comparative mitogenomic analyses of three scallops (Bivalvia: Pectinidae) reveal high level variation of genomic organization and a diversity of transfer RNA gene sets. BMC Res. Notes 2009, 2:69.
61. Xia X., Xie Z. DAMBE: software package for data analysis in molecular biology and evolution. J. Hered. 2001, 92:371-373.
62. Yamauchi M.M., Miya M.U., Machida R.J., Nishida M. PCR-based approach for sequencing mitochondrial genomes of decapod crustaceans, with a practical example from kuruma prawn (Marsupenaeus japonicus). Mar. Biotechnol. 2004, 6:419-429.