The analysis of the complete mitochondrial genome of Lecanicillium muscarium (synonym Verticillium lecanii) suggests a minimum common gene organization in mtDNAs of Sordariomycetes: Phylogenetic implications

Fungal Genetics and Biology

Volumn 41, Issue 10, 2004, Pages 930-940

  Kouvelis, Vassili N ^a   Ghikas, Dimitri V ^a   Typas, Milton A ^a  

^a UNIVERSITY OF ATHENS   (Greece)

Author keywords

Lecanicillium muscarium (synonym Verticillium lecanii); Mitochondrial gene order comparison; Mitochondrial genome organization; mtDNA, mitochondrial DNA; Phylogenetic relationships

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; CODON; CONTROLLED STUDY; FUNGAL GENE; FUNGUS; GENE MAPPING; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENOME; LECANICILLIUM MUSCARIUM; MITOCHONDRION; MOLECULAR RECOGNITION; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATIVE PHOSPHORYLATION; PHYLOGENY; PRIORITY JOURNAL;

CODON; DNA, INTERGENIC; DNA, MITOCHONDRIAL; GENE ORDER; GENES, FUNGAL; MITOCHONDRIA; MOLECULAR SEQUENCE DATA; PHYLOGENY; REGULATORY SEQUENCES, NUCLEIC ACID; RNA, TRANSFER; SEQUENCE ANALYSIS, DNA; SYNTENY; VERTICILLIUM;

FUNGI; HYPOCREALES; PEZIZOMYCOTINA; SORDARIOMYCETES; TORRUBIELLA CONFRAGOSA;

EID: 4444293373     PISSN: 10871845     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fgb.2004.07.003     Document Type: Article

References (65)

1. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and T.J. Lipaman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402
2. J.W.O. Ballard, and M.C. Whitlock The incomplete natural history of mitochondria Mol. Ecol. 13 2004 729 744
3. M.L. Berbee, D.A. Carmean, and K. Winka Ribosomal DNA and resolution of branching order among Ascomycota: how many nucleotides are enough Mol. Phylogenet. Evol. 17 2000 337 344
4. M.L. Berbee, and J.W. Taylor Dating the evolutionary origin of true fungi Can. J. Bot. 71 1993 1114 1127
5. M.L. Berbee, and J.W. Taylor Fungal molecular evolution: gene trees and geologic time D.J. McLaughlin E.G. McLaughlin P.A. Lemke The Mycota VII part B: Systematics and Evolution 2001 Springer-Verlag Berlin, Heidelberg 229 245
6. H. Bertrand Role of mitochondrial DNA in the senescence and hypovirulence of fungi and potential for plant disease control Ann. Rev. Phytopathol. 38 2000 397 422
7. J.L. Boore Animal mitochondrial genomes Nucleic Acids Res. 27 1999 1767 1780
8. C.A. Breitenberger, K.S. Browning, B. Alzner-DeWeerd, and U.L. RajBhandary RNA processing in Neurospora crassa mitochondria: use of transfer RNA sequences as signals EMBO J. 4 1985 185 195
9. C.E. Bullerwell, G. Burger, and F. Lang A novel motif for identifying Rps3 homologs in fungal mitochondrial genomes TIBS 25 2000 363 365
10. C.E. Bullerwell, L. Forget, and F. Lang Evolution of monoblepharidalean fungi based on complete mitochondrial sequences Nucleic Acids Res. 31 2003 1614 1623
11. C.E. Bullerwell, C.E. Leigh, L. Forget, and F. Lang A comparison of three fission yeast mitochondrial genomes Nucleic Acids Res. 31 2003 759 768
12. G. Burger, M.W. Gray, and B.F. Lang Mitochondrial genomes: anything goes Trends Genet. 19 2003 709 716
13. T.M Butt, C.W Jackson, and N. Magan Fungi as biocontrol agents 2001 CABI Publishing Walingford, UK
14. A. Cambell, J. Mrazek, and S. Karlin Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA Proc. Natl. Acad. Sci. USA 96 1999 9184 9189
15. J.J. Cannone, S. Subramanian, M.N. Schnare, J.R. Colett, L.M. D'Souza, Y. Du, B. Feng, N. Lin, L.V. Madabusi, K.M. Muller, N. Pande, Z. Shang, N. Yu, and R.R. Gutell The Comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs BMC Bionform. 3 2002 2
16. G.D. Clark-Walker Evolution of mitochondrial genomes in fungi D.R. Welstenholme K.W. Jeon Mitochondrial Genomes 1992 Academic Press San Diego 89 127
17. D.J. Cummings, K.L. McNally, J.M. Domenico, and E.T. Matsuura The complete DNA sequence of the mitochondrial genome of Podospora anserina Curr. Genet. 17 1990 375 402
18. M. de Zamaroczy, and G. Bernardi The GC clusters of the mitochondrial genome of yeast and their evolutionary origin Gene 41 1986 1 22
19. C.W. Dieffenbach, T.M.J. Lowe, and G.S. Dveksler General concepts for PCR primer design C.W. Dieffenbach G.S. Dveksler PCR Primer: A Laboratory Manual 1995 Cold Spring Harbor Laboratory Press New York 133 142
20. J. Felsenstein Cases in which parsimony or compatibility methods will be positively misleading Syst. Zool. 25 1978 401 410
21. J. Felsenstein Confidence limits on phylogenies: an approach using the bootstrap Evolution 39 1985 783 791
22. Felsenstein, J., 2002. PHYLIP (Phylogeny Inference Package) version 3.6a3. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle
23. D.S. Fields, and R.R. Gutell An analysis of large rRNA sequences folded by a thermodynamic method Fold Des. 1 1996 419 430
24. L. Forget, J. Ustinova, Z. Wang, A.R. Huss, and F.B. Lang Hyaloraphidium curvatum: a linear mitochondrial genome, tRNA editing, and an evolutionary link to lower fungi Mol. Biol. Evol. 19 2002 310 319
25. T.D. Fox Natural variation in the genetic code Ann. Rev. Genet. 21 1987 67 91
26. M.W. Gray, G. Burger, and F.B. Lang Mitochondrial evolution Science 283 1999 1476 1481
27. W. Gams, and R. Zare A revision of Verticillium sect. Prostrata. III. Generic classification Nova Hedw. 72 2001 329 337
28. M. Hur, W.J. Geese, and R.B. Warig Self-splicing activity of the mitochondrial group-I introns from Aspergillus nidulans and related introns from other species Curr. Genet. 32 1997 399 407
29. Y. Jun, P.D. Bridge, and H.C. Evans An integrated approach to the taxonomy of the genus Verticillium J. Gen. Microbiol. 137 1991 1437 1444
30. P.J. Keeling, M.A. Luker, and J.D. Palmer Evidence from beta-tubulin phylogeny that microsporidia evolved from within the fungi Mol. Biol. Evol. 17 2000 23 31
31. J. Kleidon, N. Plesofsky, and R. Brambl Transcripts and transcript-binding proteins in mitochondria of Neurospora crassa Mitochondrion 2 2003 345 360
32. H.G. Köchel, and H. Küntzell Mitochondrial l-rRNA from Aspergillus nidulans: potential secondary structure and evolution Nucleic Acids Res. 10 1982 4795 4801
33. O.A. Kolesnikova, N.S. Entelis, H. Mireau, T.D. Fox, R.P. Martin, and I.A. Tarassov Suppression of mutations in mitochondrial DNA by tRNAs imported from the cytoplasm Science 289 2000 1931 1933
34. F. Koll, J. Boulay, L. Belcour, and Y. d'Aubenton-Carafa Contribution of ultra-short invasive elements to the evolution of the mitochondrial genome in the genus Podospora Nucleic Acids Res. 24 1996 1734 1741
35. M. Korab-Laskowska, P. Rioux, N. Brossard, T.G. Littlejohn, M.W. Gray, F.B. Lang, and G. Burger The Organelle Genome Database Project (GOBASE) Nucleic Acids Res. 26 1998 138 144
36. V.N. Kouvelis, R. Zare, P.D. Bridge, and M.A. Typas Differentiation of mitochondrial subgroups in the Verticillium lecanii species complex Lett. Appl. Microbiol. 28 1999 263 268
37. A.R. Kubelik, J.C. Kenell, R.A. Akins, and A.M. Lambowitz Identification of Neurospora mitochondrial promoters and analysis of synthesis of the mitochondrial small rRNA in wild-type and the promoter mutant [poky] J. Biol. Chem. 265 1990 4515 4526
38. M.-J. Laforest, I. Roewer, and F. Lang Mitochondrial tRNAs in the lower fungus Spizellomyces punctatus: tRNA editing and UAG 'stop' codons recognized as leucine Nucleic Acids Res. 25 1997 626 632
39. B.F. Lang, G. Burger, C.J. O'Kelly, R. Cedergren, G.B Golding, C. Lemieux, D. Sankoff, M. Turmel, and M.W. Gray An ancestral mitochondrial DNA resembling a eubacterial genome in miniature Nature 387 1997 493 497
40. B.F. Lang, M.W. Gray, and G. Burger Mitochondrial genome evolution and the origin of eukaryotes Annu. Rev. Genet. 33 1999 351 397
41. B.F. Lang, E. Sheif, M.W. Gray, C.J. O'Kelly, and G. Burger A comparative genomics approach to the evolution of eukaryotes and their mitochondria J. Eukaryot. Microbiol. 46 1999 320 326
42. C. Moritz, T.E. Dowling, and W.E. Brown Evolution of animal mitochondrial DNA: relevance for population and systematics Annu. Rev. Ecol. Syst. 18 1987 269 292
43. H. Nishida, and J. Sugiyama Phylogenetic relationships among Taphrina, Saitoella and other higher fungi Mol. Biol. Evol. 10 1993 431 436
44. B. Paquin, L. Forget, I. Roewer, and B.F. Lang Molecular phylogeny of Allomyces macrogynus: congruency between nuclear ribosomal RNA- and mitochondrial protein-based trees J. Mol. Evol. 41 1995 657 665
45. B. Paquin, M.-J. Laforest, L. Forget, I. Roewer, Z. Wang, J. Longcore, and F. Lang The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression Curr. Genet. 31 1997 380 395
46. B. Paquin, and B.F. Lang The mitochondrial DNA of Allomyces macrogynus: the complete genomic sequence from an ancestral fungus J. Mol. Biol. 255 1996 688 701
47. T.A. Pfeifer, D.D. Hegedus, and G.G. Khachatourians The mitochondrial genome of the entomopathogenic fungus Beauveria bassiana: analysis of the ribosomal RNA region Can. J. Microbiol. 39 1993 25 31
48. D.M. Roberts, B.W. Bainbridge, H.C. Evans, and J.B. Heale Genome analysis in isolates of Verticillium, V. alboatrum, V. dahliae and V. lecanii Phytoparasitica 23 1995 40
49. S. Saccone, C. Gissi, A. Reyes, A. Larizza, E. Sbisa, and G. Pesole Mitochondrial DNA in metazoa: degree of freedom in a frozen event Gene 286 2002 3 12
50. J. Sambrook, E.F. Fritsch, and T. Maniatis Molecular Cloning: A Laboratory Manual second ed. 1989 Cold Spring Harbor Laboratory New York
51. F. Sanger, S. Nicklen, and A.R. Coulson DNA sequencing with chain-termination inhibitors Proc. Natl. Acad. Sci. USA 74 1977 5463 5467
52. B. Schafer Genetic conservation versus variability in mitochondria: the architecture of the mitochondrial genome in the petite-negative yeast Schizosaccharomyces pombe Curr. Genet. 43 2003 311 326
53. T. Sekito, K. Okamoto, H. Kitano, and K. Yoshida The complete mitochondrial DNA sequence of Hansenula wingei reveals new characteristics of yeast mitochondria Curr. Genet. 28 1995 39 53
54. P.M. Sharp, T.M. Tuohy, and K.R. Mosurski Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes Nucleic Acids Res. 14 1986 5125 5143
55. M. Sugimoto, M. Koike, N. Hiyama, and H. Nagao Genetic, morphological, and virulence characterization of the entomopathogenic fungus Verticillium lecanii J. Invertebr. Pathol. 82 2003 176 187
56. Swofford, D.L., 1998. PAUP*. Phylogenetic Analysis using Parsimony (*) and other methods, version 4. Sinauer Associates, Sunderland, MA
57. J.-W. Taanman The mitochondrial genome: structure, transcription, translation and replication Biochim. Biophys. Acta 1410 1999 103 123
58. J.D. Thompson, D.G. Higgins, and T.J. Gibson CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice Nucleic Acids Res. 22 1994 4673 4680
59. M.A. Typas, A.M. Griffen, B.W. Bainbridge, and J.B. Heale Restriction fragment length polymorphisms in mitochondrial DNA and ribosomal RNA gene complexes as an aid to the characterization of species and sub-species populations in the genus Verticillium FEMS Microbiol. Lett. 95 1992 157 162
60. M.A. Typas, M. Pantou, and D. Ghikas Genetic fingerprinting tools and comparisons of entomopathogenic fungi M. Vurro J. Gressel T. Butt G.E. Harman A. Pilgeram R.J. StLeger D.L. Nuss Enhancing Biocontrol Agents and Handling Risks 2001 IOS Press Amsterdam 217 228
61. T.J. White, T.D. Bruns, S. Lee, and J. Taylor Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics M.A. Innis D.H. Gelfand J.J. Sninsky T.J. White PCR Protocols 1990 Academic Press San Diego 315 322
62. Z. Yang PAML: a program package for phylogenetic analysis by maximum likelihood CABIOS 13 1997 555 556
63. R. Zare, and Gams A revision of Verticillium section Prostrata. IV. The genera Lecanicillium and Simplicillium gen. nov Nova Hedw. 73 2001 1 50
64. R. Zare, W. Gams, and A. Culham A revision of Verticillium sect. Prostrata I. Phylogenetic studies using ITS sequences Nova Hedw. 71 2000 465 480
65. R. Zare, V.N. Kouvelis, P.D. Bridge, and M.A. Typas Presence of a 20 bp insertion/deletion in the ITS1 region of Verticillium lecanii Lett. Appl. Microbiol. 28 1999 258 262