The complete mitochondrial genome of Fusarium oxysporum: Insights into fungal mitochondrial evolution

Gene

Volumn 419, Issue 1-2, 2008, Pages 7-15

  Pantou, Malena P ^a   Kouvelis, Vassili N ^a   Typas, Milton A ^a  

^a UNIVERSITY OF ATHENS   (Greece)

Author keywords

Gene order; Mitochondrial DNA; Pezizomycotina; Sordariomycetes

Indexed keywords

AMINO ACID; MITOCHONDRIAL DNA; NUCLEOTIDE; PROTEIN; RIBOSOME RNA; TRANSFER RNA;

ARTICLE; ASCOMYCETES; COMPARATIVE STUDY; CONTROLLED STUDY; DNA SEQUENCE; FUNGAL GENE; FUNGAL STRAIN; FUSARIUM OXYSPORUM; GENE ORDER; INTROSPECTION; MITOCHONDRIAL GENE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PEZIZOMYCOTINA; PHYLOGENY; PHYLUM; PRIORITY JOURNAL; RNA GENE; SORDARIOMYCETES; TAXONOMY;

CODON; DNA, INTERGENIC; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; FUSARIUM; GENE ORDER; GENES, FUNGAL; GENOME, MITOCHONDRIAL; PHYLOGENY;

FUNGI; FUSARIUM OXYSPORUM; HYPOCREALES; PEZIZOMYCOTINA; SORDARIOMYCETES;

EID: 46149105882     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2008.04.009     Document Type: Article

References (49)

1. Abascal F., Zardoya R., and Posada D. ProtTest: selection of best fit models of protein evolution. Bioinformatics 21 (2005) 2104-2105
2. Altschul S.F., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
3. Belfort M., and Perlman P.S. Mechanisms of intron mobility. J. Biol. Chem. 270 (1995) 30237-30240
4. Berbee M.L. Loculoascomycete origins and evolution of filamentous Ascomycete morphology based on 18S rRNA gene sequence data. Mol. Biol. Evol. 13 (1996) 462-470
5. Berbee M.L., Carmean D.A., and Winka K. Ribosomal DNA and resolution of branching order among the Ascomycota: how many nucleotides are enough?. Mol. Phylogenet. Evol. 17 (2000) 337-344
6. Boore J.L., and Brown W.M. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Curr. Opin. Genet. Dev. 8 (1998) 668-674
7. Bullerwell C.E., Leigh C.E., Forget L., and Lang F. A comparison of three fission yeast mitochondrial genomes. Nucleic Acids Res. 31 (2003) 759-768
8. Clark-Walker G.D. Evolution of mitochondrial genomes in fungi. Int. Rev. Cytol. 141 (1992) 89-127
9. Eriksson O.E. Outline of Ascomycota - 2006. Myconet 12 (2006) 1-82
10. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (1985) 783-791
11. Felsenstein J. PHYLIP (Phylogeny Inference Package) version 3.6a3. Distributed by the author (2002), Department of Genome Sciences, University of Washington, Seattle
12. Fitzpatrick D.A., Logue M.E., Stajich J.E., and Butler G. A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol. Biol. 6 (2006) 10.1186/1471-2148-6-99
13. Ghikas D.V., Kouvelis V.N., and Typas M.A. The complete mitochondrial genome of the entomopathogenic fungus Metarhizium anisopliae var. anisopliae: gene order and trn gene clusters reveal a common evolutionary course for all Sordariomycetes. Arch. Microbiol. 185 (2006) 393-401
14. Gray M.W., Burger G., and Lang B.F. Mitochondrial evolution. Science 283 (1999) 1476-1481
15. Hackett S.J. Molecular phylogenetics and biogeography of tanagers in the genus Ramphocelus (Aves). Mol. Phylogenet. Evol. 5 (1996) 368-382
16. Hamari Z., Juhasz A., Gacser A., Kucsera J., Pfeiffer I., and Kevei F. Intron mobility results in rearrangement in mitochondrial DNAs of heterokaryon incompatible Aspergillus japonicus strains after protoplast fusion. Fungal Genet. Biol. 33 (2001) 83-95
17. Hibbett D.S., et al. A higher-level phylogenetic classification of the fungi. Mycol. Res. 111 (2007) 509-547
18. Keeling P.J., Luker M.A., and Palmer J.D. Evidence from beta tubulin phylogeny that microsporidia evolved from within the fungi. Mol. Biol. Evol. 17 (2000) 23-31
19. Kistler H.C. Evolution of host specificity in Fusarium oxysporum. In: Summerell B.A., Leslie J.F., Backhouse D., Bryden W.L., and Burgess L.W. (Eds). Fusarium. Paul E. Nelson Memorial Symposium (2001), APS Press, Minnesota 70-82
20. Kouvelis V.N., Ghikas D.V., and Typas M.A. 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 Genet. Biol. 41 (2004) 930-940
21. Kumazawa Y., Ota H., Nishida M., and Ozawa T. The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions. Genetics 150 (1998) 313-329
22. Kuramae E.E., Robert V., Snel B., and Boekhout T. Conflicting phylogenetic position of Schizosaccharomyces pombe. Genomics 88 (2006) 387-393
23. Lowe T.M., and Eddy S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25 (1997) 955-964
24. Liu Y.J., and Hall B.D. Body plan evolution of ascomycetes, as inferred from an RNA polymerase II phylogeny. Proc. Natl. Acad. Sci. U. S. A. 101 13 (2004) 4507-4512
25. Lumbsch H.T., Wirtz N., Lindemuth R., and Schmitt I. Higher level phylogenetic relationships of euascomycetes (Pezizomycotina) inferred from a combined analysis of nuclear and mitochondrial sequence data. Mycol. Progr. 1 (2002) 57-70
26. Lumbsch H.T., et al. Performance of four ribosomal DNA regions to infer higher level phylogenetic relationships of inoperculate euascomycetes (Leotiomyceta). Mol. Phylogenet. Evol. 34 (2005) 512-524
27. Lutzoni F., et al. Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. Am. J. Bot. 91 (2004) 1446-1480
28. Osiewacz H.D. Genes, mitochondria and aging in filamentous fungi. Ageing Res. Rev. 1 (2002) 425-442
29. Pantou M.P., Kouvelis V.N., and Typas M.A. The complete mitochondrial genome of the vascular wilt fungus Verticillium dahliae: a novel gene order for Verticillium and a diagnostic tool for species identification. Curr. Genet. 50 (2006) 125-136
30. Pantou M.P., Strunnikova O.K., Shakhnazarova V.Y., Vishnevskaya N.A., Papalouka V.G., and Typas M.A. Molecular and immunochemical phylogeny of Verticillium species. Mycol. Res. 109 (2005) 889-902
31. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
32. Posada D., and Buckley T.R. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53 (2004) 793-808
33. Pramateftaki P.V., Kouvelis V.N., Lanaridis P., and Typas M.A. The mitochondrial genome of the wine yeast Hanseniaspora uvarum: a unique genome organization among yeast/fungal counterparts. FEMS Yeast Res. 6 (2006) 77-90
34. Reeb V., Lutzoni F., and Roux C. Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory. Mol. Phylogenet. Evol. 32 (2004) 1036-1060
35. Robbertse B., Reeves J.B., Schoch C.L., and Spatafora J.W. A phylogenomic analysis of the Ascomycota. Fungal Genet. Biol. 43 (2006) 715-725
36. Rokas A., Williams B.L., King N., and Carroll S.B. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425 (2003) 798-804
37. Ronquist F.R., and Huelsenbeck J.P. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
38. Saccone S., Gissi C., Reyes A., Larizza A., Sbisa E., and Pesole G. Mitochondrial DNA in metazoa: degree of freedom in a frozen event. Gene 286 (2002) 3-12
39. Shimodaira H., and Hasegawa M. CONSEL: a program for assessing the confidence of phylogenetic tree selection. Bioinformatics 17 (2001) 1246-1247
40. Spatafora J.W., et al. A five-gene phylogeny of Pezizomycotina. Mycologia 98 (2006) 1018-1028
41. Swofford D.L. PAUP: Phylogenetic Analysis Using Parsimony (*and other methods) 4.0 Beta (2002), Sinauer, Sunderland, MA
42. Tambor J.H., Guedes R.F., Nobrega M.P., and Nobrega F.G. The complete DNA sequence of the mitochondrial genome of the dermatophyte fungus Epidermophyton floccosum. Curr. Genet. 49 (2006) 302-308
43. Tehler A., Little D.P., and Farris J.S. The full-length phylogenetic tree from 1551 ribosomal sequences of chitinous fungi, Fungi. Mycol. Res. 107 8 (2003) 901-916
44. Thompson J.D., Higgins D.G., and 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. 22 (1994) 4673-4680
45. Typas M.A., Griffen A.M., Bainbridge B.W., and Heale J.B. 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
46. Wang Z., Binder M., Schoch C.L., Johnston P.R., Spatafora J.W., and Hibbett D.S. Evolution of helotialean fungi (Leotiomycetes, Pezizomycotina): a nuclear rDNA phylogeny. Mol. Phylogenet. Evol. 41 (2006) 295-312
47. White T.J., Bruns T.D., Lee S., and Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M.A., Gelfand D.H., Sninsky J.J., and White T.J. (Eds). PCR Protocols (1990), Academic Press, San Diego 315-322
48. Xia X., and Xie Z. DAMBE: data analysis in molecular biology and evolution. J. Heredity 92 (2001) 371-373
49. Yang Z. Among-site rate variation and its impact on phylogenetic analyses. TREE 11 (1996) 367-372