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  • Aanen DK, Kuyper TW, Hoekstra RF (2001) A widely distributed ITS polymorphism within a biological species of the ectomycorrhizal fungus Hebeloma velutipes. Mycological Research, 105, 284290.
  • Aime CM, Matheny BP, Henk DA et al . (2006) An overview of the higher level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences. Mycologia, 98, 896905.
  • Ballard JWO, Whitlock MC (2004) The incomplete natural history of mitochondria. Molecular Ecology, 13, 729744.
  • Bateman A, Coin L, Durbin R et al . (2004) The Pfam protein families database. Nucleic Acids Research, 32, D138D141.
  • Bridge PD, Spooner BM, Roberts PJ (2005) The impact of molecular data in fungal systematics. Advances in Botanical Research, 42, 3467.
  • Brudno M, Malde S, Poliakov A et al . (2003) Glocal alignment: finding rearrangements during alignment. Bioinformatics 19, i54i62.
  • Bruns TD (2001) ITS reality. Inoculum, 52, 2.
  • Bruns TD, White TJ, Taylor TJ (1991) Fungal molecular systematics. Annual Review of Ecology and Systematics, 22, 525564.
  • Bullerwell CE, Lang FB (2005) Fungal evolution: the case of the vanishing mitochondrion. Current Opinion in Microbiology, 8, 362369.
  • Bullerwell CE, Leigh J, Forget L, Lang FB (2003) A comparison of three fission yeast mitochondrial genomes. Nucleic Acids Research, 31, 759768.
  • Burger G, Gray MW, Lang FB (2003) Mitochondrial genomes: anything goes. Trends in Genetics, 19, 709716.
  • Chillali M, Idder-Ighili H, Guillaumin JJ et al . (1998) Variation in the ITS and IGS regions of ribosomal DNA among the biological species of European Armillaria. Mycological Research, 102, 533540.
  • Collins TM, Wimberger PH, Naylor GJP (1994) Compositional bias, character-state bias, and character-state reconstruction using parsimony. Systematic Biology, 43, 482496.
  • Coprinus Cinereus Sequencing Project. Broad Institute of MIT and Harvard  http://www.broad.mit.edu .
  • Crane PE (2001) Morphology, taxonomy, and nomenclature of the Chrysomyxa ledi complex and related rust fungi on spruce and Ericaceae in North America and Europe. Canadian Journal of Botany, 79, 957982.
  • Cryptococcus neoformans Genome Project, B3501A assembly data, Stanford Genome Technology Center, funded by the NIAID/NIH under cooperative agreement AI47087, and The Institute for Genomic Research, funded by the NIAID/NIH under cooperative agreement U01 AI48594. http://www-sequence.stanford.edu/group/C.neoformans/ .
  • Cryptococcus Neoformans Serotype B Sequencing Project. Broad Institute of MIT and Harvard. http://www.broad.mit.edu .
  • Cummings MP, Otto SP, Wakeley J (1995) Sampling properties of DNA sequence data in phylogenetic analysis. Molecular Biology and Evolution, 12, 814822.
  • Cywinska A, Hunter FF, Hebert PDN (2006) Identifying Canadian mosquito species through DNA barcodes. Medical and Veterinary Entomology, 20, 413424.
  • Dalgaard JZ, Klar AJ, Moser MJ et al . (1997) Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family. Nucleic Acids Research, 25, 46264638.
  • Eddy SR (1998) Profile hidden Markov models. Bioinformatics, 14, 755763.
  • Foster PG, Hickey DA (1999) Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. Journal of Molecular Evolution, 48, 284290.
  • Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts. Molecular Ecology, 2, 113118.
  • Grasso V, Sierotzki H, Gisi U (2006) Relatedness among agronomically important rusts based on mitochondrial cytochrome b gene and ribosomal ITS sequences. Journal of Phytopathology, 154, 110118.
  • Guarro J, Gene J, Stchigel AM (1999) Developments in fungal taxonomy. Clinical Microbiology Reviews, 12, 454500.
  • Hajibabaei M, DeWaard JR, Ivanova N et al . (2005) Critical factors for assembling a high volume of DNA barcodes. Philosophical Transactions of the Royal Society B: Biological Sciences, 360, 19591967.
  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41, 9598.
  • Heath PJ, Stephens KM, Monnat RJ, Stoddard BL (1997) The structure of I-CreI, a Group I intron-encoded homing endonuclease. Nature Structural Biology, 4, 468476.
  • Hebert PDN, Cywinska A, Ball SL, DeWaard JR (2003) Biological identifications through DNA barcodes. Philosophical Transactions of the Royal Society B: Biological Sciences, 270, 313321.
  • Hebert PDN, Gregory TR (2005) The promise for DNA barcoding for taxonomy. Systematic Biology, 54, 852859.
  • Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W (2004a) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgetor. Proceedings of the National Academy of Sciences, USA, 101, 1481214817.
  • Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004b) Identification of birds through DNA barcodes. Public Library of Science, Biology, 2, 16571663.
  • Hibbet DS, Binder M, Bischoff JF et al . (2007) A higher-level phylogenetic classification of the Fungi. Mycological Research, 111, 509547.
  • Hofstetter V, Miadlikowska J, Gueidan C et al . (2004) What do protein-coding genes (ATP6, EF1-alpha and RNA polymerase II) bring to molecular systematics of lichens?. In: Book of Abstracts of the 5th IAL Symposium: Lichens in Focus (ed. PressTU), p. 15. Tartu University Press, Tartu, Estonia.
  • Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Research, 9, 868877.
  • Huang X, Yang S-P, Chinwalla AT et al . (2006) Application of a superword array in genome assembly. Nucleic Acids Research, 34, 201205.
  • Ihako R, Gentleman R (1996) r: a language for data analysis and graphics. Journal of Computational and Graphical Statistics, 5, 299314.
  • IRGSP (2005) The map-based sequence of the rice genome. Nature, 436, 793800.
  • James T, Kauff F, Schoch CL et al . (2006) Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature, 443, 818822.
  • Katsu M, Kidd S, Ando A et al . (2004) The internal transcribed spacers and 5.8S rRNA gene show extensive diversity among isolates of the Cryptococcus neoformans species complex. FEMS Yeast Research, 4, 377388.
  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111120.
  • Kirk PM, Cannon PF, David JC, Stalpers JA (2001) Dictionary of the Fungi, 9th edn. CABI Publishing, Wallingford, UK.
  • Klich MA, Mullaney EJ (1992) Molecular methods for identification and taxonomy of filamentous fungi. In: Handbook of Applied Mycology (ed. AroraDK), pp. 3557. Banara Hindu University, Varanasi, India.
  • Kouvelis VN, Ghikas DV, Typas MA (2004) 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, 41, 930940.
  • Kretzer AM, Bruns TD (1999) Use of atp6 in fungal phylogenetics: an example from the Boletales. Molecular Phylogenetics and Evolution, 13, 483492.
  • Lang FB, Laforest M-J, Burger G (2007) Mitochondrial introns: a critical view. Trends in Genetics, 23, 119125.
  • Lim YW, Sturrock R, Leal I et al . (2008) Distinguishing homokaryons and heterokaryons in Phellinus sulphurascens using pairing tests and ITS polymorphisms. Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 93, 99110.
  • Lin JJ, Garber RC, Yoder OC (1988) Nucleotide sequence of a fungal plasmid-like DNA containing the mitochondrial ATPase subunit 6 gene. Nucleic Acids Research, 16, 9875.
  • Lockhart PJ, Steel MA, Hendy MD, Penny D (1994) Recovering evolutionary trees under a more realistic model of sequence evolution. Molecular Biology and Evolution, 11, 605612.
  • Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research, 25, 955964.
  • Lutzoni F, Kauff F, Cox JC et al . (2004) Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. American Journal of Botany, 91, 14461480.
  • Martin F, Aerts A, Ahren D et al . (2008) The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature, 452, 8892.
  • Martin FN, Bensasson D, Tyler BM (2007) Mitochondrial genome sequences and comparative genomics of Phytophtora ramorum and P. sojae. Current Genetics, 51, 285296.
  • Matheny PB, Wang Z, Binder M et al . (2007) Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi). Molecular Phylogenetics and Evolution, 43, 430451.
  • Mayor C, Brudno M, Schwartz JR et al . (2000) VISTA: vizualizing global DNA sequence alignments of arbitrary length. Bioinformatics Applications Note, 16, 10461047.
  • Min XJ, Hickey DA (2007) Assessing the effect of varying sequence length on DNA barcoding of fungi. Molecular Ecology Notes, 7, 365373.
  • Mohr G, Perlman PS, Lambowitz AM (1993) Evolutionary relationships among groupII intron-encoded proteins and identification of a conserved domain that may be related to maturase function. Nucleic Acids Research, 21, 49914997.
  • Moriyama EN, Powell JR (1997) Synonymous substitution rates in Drosophila: mitochondrial versus nuclear genes. Journal of Molecular Evolution, 45, 378391.
  • Mourrier T, Hansen AJ, Willerslev E, Arctander P (2001) The human genome project reveals a continuous transfer of large mitochondrial fragments to the nucleus. Molecular Biology and Evolution, 18, 18331837.
  • O'Donnell K, Cigelnik E (1997) Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous. Molecular Phylogenetics and Evolution, 7, 103116.
  • Okabe I, Matsumoto N (2003) Phylogenetic relationship of Sclerotium rolfsil (teleomorph Athelia rolfsii) and S.delphinii based on ITS sequences. Mycological Research, 107, 164168.
  • Pamilo P, Viljakainen L, Vihavainen A (2007) Exceptionally high density of numts in the honeybee genome. Molecular Biology and Evolution, 24, 13401346.
  • Pantou M, Kouvelis V, Typas M (2006) The complete mitochondrial genome of the vascular wilt fungus Verticillium dahliae: a novel gene order for Verticillium and a diagnostic tool for species identification. Current Genetics, 50, 125136.
  • Paquin B, Laforest M-J, Forget L et al . (1997) The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression. Current Genetics, 31, 380395.
  • Paquin B, O’Kelly CJ, Lang FB (1995) Intron-encoded open reading frame of the GIY-YIG subclass in a plastid gene. Current Genetics, 28, 9799.
  • Pei MH, Shang YZ (2005) A brief summary of Melampsora species on Populus. In: Rust Disease of Willow and Poplar (eds PeiMH, McCrackenAR), pp. 5161. CABI Publishing, Wallingford, UK.
  • Posada D, Crandall KA (1998) ModelTest: testing the model of DNA substitution. Bioinformatics, 14, 817818.
  • Puccinia Graminis Sequencing Project. Broad Institute of MIT and Harvard. http://www.broad.mit.edu .
  • Ricchetti M, Fairhead C, Dujon B (1999) Mitochondrial DNA repairs double-stand breaks in yeast chromosomes. Nature, 402, 96100.
  • Richly E, Leister D (2004) NUMTs in sequenced eukaryotic genomes. Molecular Biology and Evolution, 21, 10811084.
  • Roe AD, Sperling FAH (2007) Patterns of evolution of mitochondrial cytochrome c oxidase I and II DNA and implication for DNA barcoding. Molecular Phylogenetics and Evolution, 44, 325345.
  • Rokas A, Nylander JAA, Ronquist F, Stone GN (2002) A maximum-likelihood analysis of eight phylogenetic markers in gallwasps (Hymenoptera: Cynipidae): implications for insect phylogenetic studies. Molecular Phylogenetics and Evolution, 22, 206209.
  • Seifert KA, Samson RA, DeWaard JR et al . (2007) Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case. Proceedings of the National Academy of Sciences of the USA, 104, 39013906.
  • Skouboe P, Frisvad JC, Taylor JW et al . (1999) Phylogenetic analysis of nucleotide sequences from the ITS region of terverticillate Penicillium species. Mycological Research, 103, 873881.
  • Smith M, Douhan G, Rizzo D (2007) Intra-specific and intra-sporocarp ITS variation of ectomycorrhizal fungi as assessed by rDNA sequencing of sporocarps and pooled ectomycorrhizal roots from a Quercus woodland. Mycorrhiza, 18, 1522.
  • Song H, Buhay JE, Whiting MF, Crandall KA (2008) Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proceedings of the National Academy of Sciences, USA, 105, 1348613491.
  • Stoll M, Piepenbring M, Begerow D, Oberwinkler F (2003) Molecular phylogeny of Ustilago and Sporisorium species (Basidiomycota, Ustilaginales) based on internal transcribed spacer (ITS) sequences. Canadian Journal of Botany, 81, 976984.
  • Stupar RM, Lilly JW, Town CD et al . (2001) Complex mtDNA constitutes an approximate 620-kb insertion on Arabidopsis thaliana chromosome 2: implication of potential sequencing errors caused by large-unit repeats. Proceedings of the National Academy of Sciences, USA, 98, 50995103.
  • Swofford DJ (2003) paup 4.0 User's manual: Phylogenetic Analysis Using Parsimony. Sinauer Associates Inc., Sunderland, Massachusetts.
  • Thompson JD, Higgins DG, Gibson TJ (1994) ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22, 46734680.
  • Tian G-L, Michel F, Macadre C, Slonimski PP, Lazowska J (1991) Incipient mitochondrial evolution in yeasts II. Journal of Molecular Biology, 218, 747760.
  • Tian C-M, Shang Y-Z, Zhuang J-Y, Wang Q, Kakishima M (2004) Morphological and molecular phylogenetic analysis of Melampsora species on poplars in China. Mycoscience, 45, 5666.
  • Toor N, Zimmerly S (2002) Identification of a family of group II introns encoding LAGLIDADG ORFs typical of group I introns. RNA, 8, 13731377.
  • Vaughn JC, Mason MT, Sper-Whitis GL, Kulman P, Palmer JD (1995) Fungal origin by horizontal transfer of a plant mitochondrial group I intron in the chimeric Cox1 gene of Peperomia. Journal of Molecular Evolution, 41, 563572.
  • Vilgalys R, Hester M (1990) Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. Journal of Bacteriology, 172, 42384246.
  • Waugh J (2007) DNA barcoding in animal species: progress, potential and pitfalls. Bioessays, 29, 188197.
  • White TJ, Bruns TS, Lee S, Taylor JW (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR Protocols: A Guide to Methods and Applications (eds InnisMA, GelfandDH, SninskyJJ, WhiteTJ), pp. 315322. Academic Press, New York.
  • Xu J, Singh RS (2005) The inheritance of organelle genes and genomes: patterns and mechanisms. Genome, 48, 951958.
  • Yan Z, Xu J (2005) Fungal mitochondrial inheritance and evolution. In: Evolutionary Genetics of Fungi (ed. XuJ), pp. 221252. Horizon Scientific Press, Wymondham, UK.
  • Zeng JS, De Hoog GS (2008) Exophiala spinifera and its allies: diagnostics from morphology to DNA barcoding. Medical Mycology, 46, 193208.