Literature

Mitochondrial genome sequences have been analyzed fully in articles from which several arguments concerning mitogenomic and taxonomic questions are posed. In addition, mt genomes and their features, for example, single genes and intergenic regions, have been extensively used for resolving fungal phylogenetic and evolutionary relationships and for species/strain identification.

Selected articles linked to their respective entries in PubMed are provided in Tables 1-3.


Table 1: Selected articles analysing complete mitochondrial fungal genomes.

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Article Information Pubmed ID
Al-Reedy R.M., Malireddy R., Dillman C.B. and Kennell J.C. (2012). Comparative analysis of Fusarium mitochondrial genomes reveals a highly variable region that encodes an exceptionally large open reading frame.Fungal Genetics and Biology 49: 2-14. 22178648
Amlacher S., Sarges P., Flemming D., van Noort V., Kunze R., Devos D.P., Arumugam M., Bork P. and Hurt E. (2011). Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile. Cell 146: 277-289. 21784248
Anderson J.B., Wickens C., Khan M., Cowen L.E., Federspiel N., Jones T. and Kohn L.M. (2001). Infrequent genetic exchange and recombination in the mitochondrial genome of Candida albicans.  Journal of Bacteriology 183: 865-872.  11208783
Bouchier C., Ma L., Creno S., Dujon B. and Fairhead C. (2009).Complete mitochondrial genome sequences of three Nakaseomyces species reveal invasion by palindromic GC clusters and considerable size expansion. FEMS Yeast Res. 9: 1283-1292.  19758332
Bullerwell C.E., Burger G. and Lang B.F. (2000). A novel motif for identifying rps3 homologs in fungal mitochondrial genomes. Trends in Biochemical Sciences 25(8): 363-365. 10916154
Bullerwell C.E., Forget L. and Lang B.F. (2003). Evolution of monoblepharidalean fungi based on complete mitochondrial genome sequences. Nucleic Acids Research 31: 1614-1623. 12626702
Bullerwell C.E., Leigh J., Forget L. and Lang B.F. (2003). A comparison of three fission yeast mitochondrial genomes.  Nucleic Acids Research 31: 759-768. 12527786
Cardoso M.A., Tambor J.H. and Nobrega F.G. (2007). The mitochondrial genome from the thermal dimorphic fungus Paracoccidioides brasiliensis. Yeast 24: 607-616. 17492801
Chambergo F.S., Bonaccorsi E.D., Ferreira A.J., Ramos A.S., Ferreira Júnior J.R., Abrahão-Neto J., Farah J.P. and El-Dorry H. (2002). Elucidation of the metabolic fate of glucose in the filamentous fungus Trichoderma reesei using expressed sequence tag (EST) analysis and cDNA microarrays, The Journal of Biological Chemistry 277: 13983-13988. 11825887
Costa G.G., Cabrera O.G., Tiburcio R.A., Medrano F.J., Carazzolle M.F., Thomazella D.P., Schuster S.C., Carlson J.E., Guiltinan M.J., Bailey B.A., Mieczkowski P., Pereira G.A. and Meinhardt L.W. (2012). The mitochondrial genome of Moniliophthora roreri, the frosty pod rot pathogen of cacao. Fungal Biology 116: 551-562.  22559916
Costa G.G., Cabrera O.G., Tiburcio R.A., Medrano F.J., Carazzolle M.F., Thomazella D.P., Schuster S.C., Carlson J.E., Guiltinan M.J., Bailey B.A., Mieczkowski P., Pereira G.A. and Meinhardt L.W. (2012). The mitochondrial genome of Moniliophthora roreri, the frosty pod rot pathogen of cacao. Fungal Biol. 116: 551-562. 22559916
Cummings D.J., McNally K.L., Domenico J.M. and Matsuura E.T.  (1990). The complete DNA sequence of the mitochondrial genome of Podospora anserina. Current Genetics  17: 375-402. 2357736
Dietrich F.S., Voegeli S., Brachat S., Lerch A.,  Gates K., Steiner S., Mohr C., Pöhlmann R., Luedi P., Choi S., Wing R.A., Flavier A., Gaffney T.D. and Philippsen P. (2004).The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304: 304-307. 15001715
Duò A., Bruggmann R., Zoller S., Bernt M. and Grünig C.R. (2012). Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex. BMC Genomics 13: 166. 22559219
Eldarov M.A., Mardanov A.V., Beletsky A.V., Dzhavakhiya,V.V., Ravin N.V. and Skryabin K.G. (2012) Complete mitochondrial genome of compactin-producing fungus Penicillium solitum and comparative analysis of Eurotiales mitochondrial genomes. FEMS Microbiol Letters 329: 9-17. 22239643
Forget L., Ustinova J., Wang Z., Huss V.A. and Lang B.F. (2002). Hyaloraphidium curvatum: a linear mitochondrial genome, tRNA editing, and an evolutionary link to lower fungi. Molecular Biology and Evolution 19: 310-319. 11861890
Formey D., Molès M., Haouy A., Savelli B., Bouchez O., Bécard G. and Roux C. (2012). Comparative analysis of mitochondrial genomes of Rhizophagus irregularis - syn. Glomus irregulare - reveals a polymorphism induced by variability generating elements. New Phytologist 196(4): 1217-1227. 22967288
Formighieri E.F., Tiburcio R.A., Armas E.D., Medrano F.J., Shimo H., Carels N., Góes-Neto A., Cotomacci C., Carazzolle M.F., Sardinha-Pinto N., Thomazella D.P., Rincones J., Digiampietri L., Carraro D.M., Azeredo-Espin A.M., Reis S.F., Deckmann A.C., Gramacho K., Gonçalves M.S., Moura Neto J.P., Barbosa L.V., Meinhardt L.W., Cascardo J.C. and Pereira G.A. (2008). The mitochondrial genome of the phytopathogenic basidiomycete Moniliophthora perniciosa is 109 kb in size and contains a stable integrated plasmid. Mycol Res. 112: 1136-1152. 18786820
Foury F., Roganti T., Lecrenier N. and Purnelle B. (1998). The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae. FEBS Letters 440: 325-331.  9872396
Fricova D., Valach M., Farkas Z., Pfeiffer I., Kucsera J., Tomaska L. and Nosek J. (2010). The mitochondrial genome of the pathogenic yeast Candida subhashii: GC-rich linear DNA with a protein covalently attached to the 5' termini. Microbiology 156(Pt 7): 2153-2163.  20395267
Friedrich A., Jung P.P., Hou J., Neuvéglise C. and Schacherer J. (2012). Comparative mitochondrial genomics within and among yeast species of the Lachancea genus. PLoS One 7(10): e47834. 23112855
Gaillardin C., Neuveglise C., Kerscher S. and Nicaud J.M. (2012). Mitochondrial genomes of yeasts of the Yarrowia clade. FEMS Yeast Research 12, 317-331. 22188421
Ghikas D.V., Kouvelis V.N. and Typas M.A. (2006).  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, while intergenic regions show variation. Archives of Microbiology 185: 393-401.  16552580
Ghikas D.V., Kouvelis V.N. and Typas M.A. (2010). Phylogenetic and biogeographic implications inferred by mitochondrial intergenic region analyses and ITS1-5.8S-ITS2 of the entomopathogenic fungi Beauveria bassiana and B. brongniartii. BMC Microbiology 10: 174. 20553589
Hane J.K., Lowe R.G., Solomon P.S., Tan K.C.,  Schoch C.L., Spatafora J.W., Crous P.W., Kodira C., Birren B.W., Galagan J.E., Torriani S.F., McDonald B.A. and Oliver R.P. (2007)  Dothideomycete plant interactions illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorum. Plant Cell 19:  3347-3368. 18024570
Haridas S. and Gantt J.S. (2010). The mitochondrial genome of the wood-degrading basidiomycete Trametes cingulata. FEMS Microbiology Letters 308: 29-34. 20455947
Joardar V., Abrams N.F., Hostetler J., Paukstelis P.J., Pakala S., Pakala S.B., Zafar N., Abolude O.O., Payne G., Andrianopoulos A., Denning D.W. and Nierman W.C. (2012). Sequencing of mitochondrial genomes of nine Aspergillus and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability. BMC Genomics 13: 698. 23234273
Juhász A., Engi H., Pfeiffer I., Kucsera J., Vágvölgyi C. and Hamari Z. (2007).  Interpretation of mtDNA RFLP variability among Aspergillus tubingensis isolates.  Antonie Van Leeuwenhoek 91: 209-216. 17043909
Juhász A., Pfeiffer I., Keszthelyi A., Kucsera J., Vágvölgyi C. and Hamari Z. (2008). Comparative analysis of the complete mitochondrial genomes of Aspergillus niger mtDNA type 1a and Aspergillus tubingensis mtDNA type 2b. FEMS Microbiology Letters 281: 51-57. 18318841
Jung P.P., Friedrich A., Reisser C., Hou J. and Schacherer J. (2012). Mitochondrial genome evolution in a single protoploid yeast species. G3 - Genes, Genoems, Genetics 2(9): 1103-1111. 22973548
Jung P.P., Friedrich A., Souciet J.L., Louis V., Potier S., de Montigny J. and Schacherer J. (2010). Complete mitochondrial genome sequence of the yeast Pichia farinosa and comparative analysis of closely related species. Current Genetics 56(6): 507-515. 20830585
Kerscher S., Durstewitz G., Casaregola S., Gaillardin C. and Brandt U. (2001). The complete mitochondrial genome of Yarrowia lipolytica. Comparative and Functional Genomics 2: 80-90. 18628906
Kosa P., Valach M., Tomaska L., Wolfe K.H. and Nosek J. (2006). Complete DNA sequences of the mitochondrial genomes of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis: insight into the evolution of linear DNA genomes from mitochondrial telomere mutants. Nucleic Acids Research 34: 2472-2481. 16684995
Koszul,R., Malpertuy,A., Frangeul,L., Bouchier,C.,  Wincker P., Thierry A., Duthoy S., Ferris S., Hennequin C. and Dujon B. (2003). The complete mitochondrial genome sequence of the pathogenic yeast  Candida (Torulopsis) glabrata. FEBS Letters 534: 39-48. 12527359
Kouvelis V.N., Ghikas D.V. and Typas M.A. (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: 930-940.   15341915
Kuberl A., Schneider J., Thallinger G.G., Anderl I., Wibberg D., Hajek T., Jaenicke S., Brinkrolf K., Goesmann A., Szczepanowski R., Puhler A., Schwab H., Glieder A. and Pichler H. (2011). High-quality genome sequence of Pichia pastoris CBS7435. J. Biotechnol. 154: 312-320. 21575661
Laforest M.J., Bullerwell C.E., Forget L. and Lang B.F. (2004). Origin, evolution, and mechanism of 5' tRNA editing in chytridiomycete fungi. 10(8): 1191-1199. 15247432
Laforest M.J., Roewer I. and Lang B.F. (1997). Mitochondrial tRNAs in the lower fungus Spizellomyces punctatus: tRNA editing and UAG 'stop' codons recognized as leucine. Nucleic Acids Research 25(3): 626-632. 9016605
Lang B.F. and Hijri M. (2009). The complete Glomus intraradices mitochondrial genome sequence-a milestone in mycorrhizal research. New Phytologist 183(1): 3-6. 19555368
Lang B.F., Laforest M.J., Burger G. (2007).  Mitochondrial introns: a critical view. Trends in Genetics 23: 119-125. 17280737
Langkjaer R.B., Casaregola S., Ussery,D.W., Gaillardin C. and Piskur J. (2003). Sequence analysis of three mitochondrial DNA molecules reveals  interesting differences among Saccharomyces yeasts. Nucleic Acids Research 31: 3081-3091. 12799436
Lee J. and Young J.P. (2009). The mitochondrial genome sequence of the arbuscular mycorrhizal fungus Glomus intraradices isolate 494 and implications for the phylogenetic placement of Glomus. New Phytol. 183: 200-211. 19368666
Liu Y., Steenkamp E.T., Brinkmann H., Forget L., Philippe H. and Lang,B.F. (2009). Phylogenomic analyses predict sistergroup relationship of nucleariids and fungi and paraphyly of zygomycetes with significant support BMC Evol. Biol. 9: 272. 19939264
Martin N.C. and Lang B.F. (1997). Mitochondrial RNase P: the RNA family grows. Nucleic Acids Symposium Series (36): 42-44.  9478201
Miyakawa I., Okamuro A., Kinsky S., Visacka K., Tomaska L. and Nosek J. (2009). Mitochondrial nucleoids from the yeast Candida parapsilosis: expansion of the repertoire of proteins associated with mitochondrial DNA. Microbiology 155:1558-1568. 19383705
Nadimi M., Beaudet D., Forget L., Hijri M. and Lang B.F. (2012). Group I Intron-Mediated Trans-splicing in Mitochondria of Gigaspora rosea and a Robust Phylogenetic Affiliation of Arbuscular Mycorrhizal Fungi with Mortierellales. Molecular Biology and Evolution 29: 2199-2210. 22411852
Nakao Y., Kanamori T., Itoh T., Kodama Y., Rainieri S., Nakamura N., Shimonaga T., Hattori M. and Ashikari T. (2009). Genome sequence of the lager brewing yeast, an interspecies hybrid. DNA Research 16: 115-129. 19261625
Nosek J., Dinouël N., Kovac L., Fukuhara H. (1995). Linear mitochondrial DNAs from yeasts: telomeres with large tandem repetitions. Mol. Gen. Genet. 247: 61-72. 7715605
Nosek J., Novotna M., Hlavatovicova Z., Ussery D.W.,  Fajkus J. and Tomaska L. (2004). Complete DNA sequence of the linear mitochondrial genome of the pathogenic yeast Candida parapsilosis.  Molecular Genetics and Genomics 272: 173-180. 15449175
Nosek J., Rycovska A., Makhov A.M., Griffith J.D. and Tomaska L. (2005). Amplification of telomeric arrays via rolling-circle mechanism. J. Biol. Chem. 280: 10840-10845. 15657051
Nosek J., Tomaska L., Bolotin-Fukuhara M. and Miyakawa I. (2006). Mitochondrial chromosome structure: an insight from analysis of complete yeast genomes. FEMS Yeast Res. 6: 356-370. 16630276
Nowrousian M., Stajich J.E., Chu M., Engh I.,  Espagne E., Halliday K., Kamerewerd J., Kempken F., Knab B., Kuo H.C., Osiewacz H.D., Pöggeler S., Read N.D., Seiler S., Smith K.M., Zickler D., Kück U. and Freitag M. (2010). De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis. PLoS Genetics 6: E1000891. 20386741
Pantou M.P., Kouvelis V.N. and Typas M.A. (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: 125-136.  16733756
Pantou M.P., Kouvelis V.N. and Typas M.A. (2008). The complete mitochondrial genome of Fusarium oxysporum: insights into fungal mitochondrial evolution, Gene 419: 7-15. 18538510
Paquin B. and Lang B.F. (1996). The mitochondrial DNA of Allomyces macrogynus: the complete genomic sequence from an ancestral fungus. Journal of Molecular Biology 255: 688-701.  8636971
Paquin B., Laforest M.J. and Lang B.F. (2000). Double-hairpin elements in the mitochondrial DNA of Allomyces: evidence for mobility. Molecular Biology and Evolution 17(11): 1760-1768. 11070063
Pelin A., Pombert J.F., Salvioli A., Bonen L., Bonfante P. and Corradi N. (2012). The mitochondrial genome of the arbuscular mycorrhizal fungus Gigaspora margarita reveals two unsuspected trans-splicing events of group I introns. New Phytologist 194(3): 836-845.  22320438
Petersen R.F., Langkjaer R.B., Hvidtfeldt J., Gartner J., Palmen W., Ussery D.W. and Piskur J. (2002). Inheritance and organisation of the mitochondrial genome differ between two Saccharomyces yeasts. Journal of Molecular Biology 318: 627-636. 12054811
Pramateftaki P.V., Kouvelis V.N., Lanaridis P. and Typas M.A. (2008). Complete mitochondrial genome sequence of the wine yeast Candida zemplinina: intraspecies distribution of a novel group-IIB1 intron with eubacterial affiliations. FEMS Yeast Research 8: 311-327. 18081838
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 Research 6: 77-90. 16423073
Prochazka E., Franko F., Polakova S. and Sulo P. (2012). A complete sequence of Saccharomyces paradoxus mitochondrial genome that restores the respiration in S. cerevisiae. FEMS Yeast Res. 12: 819-830. 22830625
Procházka, E., Poláková, S., Piškur, J., Sulo, P. (2010). Mitochondrial genome from the facultative anaerobe and petite-positive yeast Dekkera bruxellensis contains the NADH dehydrogenase subunit genes. FEMS Yeast Research 10: 545-557.  20528950
Rycovska A., Valach M., Tomaska L., Bolotin-Fukuhara M., Nosek J. (2004). Linear versus circular mitochondrial genomes: intraspecies variability of mitochondrial genome architecture in Candida parapsilosis. Microbiology 150: 1571-1580. 15133118
Sacerdot C., Casaregola S., Lafontaine I., Tekaia F., Dujon B. and Ozier-Kalogeropoulos  O. (2008). Promiscuous DNA in the nuclear genomes of hemiascomycetous yeasts. FEMS Yeast Res. 8: 846-857. 18673395
Schafer B., Hansen M. and Lang B.F. (2005). Transcription and RNA-processing in fission yeast mitochondria, RNA 11: 785-795. 15811919
Seif E., Leigh J., Liu Y., Roewer I., Forget L. and Lang,B.F. (2005). Comparative mitochondrial genomics in zygomycetes: bacteria-like  RNase P RNAs, mobile elements, and a close source of the group I intron invasion in angiosperms. Nucleic Acids Research 33: 734-744. 15689432
Sekito T., Okamoto K., Kitano H. and Yoshida K. (1995).  The complete mitochondrial DNA sequence of Hansenula wingei reveals new characteristics of yeast mitochondria. Current Genetics 28: 39-53.  8536312
Sesterhenn T.M., Slaven B.E., Keely S.P., Smulian A.G., Lang B.F. and Cushion M.T. (2010). Sequence and structure of the linear mitochondrial genome of Pneumocystis carinii.  Molecular Genetics and Genomics 283: 63-72. 19921262
Stone, C.L., Buitrago, M.L.P., Boore, J.L., Frederick, R.D. (2010). Analysis of the complete mitochondrial genome sequences of the soybean rust pathogens Phakopsora pachyrhizi and P. meibomiae. Mycologia 102: 887-897.  20648755
Su D., Lieberman A., Lang B.F., Simonovic M., Söll D. and Ling J. (2011). An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine. Nucleic Acids Research 39(11): 4866-4874.  21321019
Sun X., Li H. and Yu D. (2011). Complete mitochondrial genome sequence of the phytopathogenic fungus Penicillium digitatum and comparative analysis of closely related species. FEMS Microbiology Letters 323(1): 29-34.  22092677
Talla E., Anthouard V., Bouchier C., Frangeul L. and Dujon B. (2005). The complete mitochondrial genome of the yeast Kluyveromyces thermotolerans. FEBS Lett. 579: 30-40. 15620687
Tambor J.H., Ribichich K.F. and Gomes S.L. (2008). The mitochondrial view of Blastocladiella emersonii.   Gene 424: 33-39. 18721866
Tambor J.H.M., Guedes R.F., Nobrega M.P. and Nobrega F.G. (2006). The complete DNA sequence of the mitochondrial genome of the Epidermophyton floccosum. Current Genetics 49: 302-308.  16450111
Torriani S.F., Goodwin S.B., Kema G.H., Pangilinan J.L. and McDonald B.A. (2008). Intraspecific comparison and annotation of two complete  mitochondrial genome sequences from the plant pathogenic fungus Mycosphaerella graminicola. Fungal Genetics and Biology 45: 628-637. 18226935
Valach M., Farkas Z., Fricova D., Kovac J., Brejova B., Vinar T., Pfeiffer I., Kucsera J., Tomaska L., Lang B.F. and Nosek J. (2011). Evolution of linear chromosomes and multipartite genomes in yeast mitochondria. Nucleic Acids Research 39(10): 4202-4219. 21266473
Valach M., Tomaska L. and Nosek J. (2008). Preparation of yeast mitochondrial DNA for direct sequence analysis.  Current Genetics 54: 105-109. 18568348
van de Sande W.W.J. (2012). Phylogenetic analysis of the complete mitochondrial genome of Madurella mycetomatis confirms its taxonomic position within the order Sordariales. PLoS ONE 7: e38654.  22701687
Wang Y., Zeng F., Hon C.C., Zhang Y. and Leung F.C. (2008). The mitochondrial genome of the Basidiomycete fungus Pleurotus ostreatus (oyster mushroom). FEMS Microbiol. Lett. 280: 34-41. 18248422
Woo P.C., Zhen H., Cai J.J., Yu J.,  Lau S.K., Wang J., Teng J.L., Wong S.S., Tse R.H., Chen R., Yang H., Liu B. and Yuen K.Y. (2003). The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeasts. FEBS Letters 555: 469-477. 14675758
Wu Y., Yang J., Yang F., Liu T.,  Leng W ., Chu Y. and Jin Q. (2009).  Recent dermatophyte divergence revealed by comparative and phylogenetic analysis of mitochondrial genomes BMC Genomics 10: 238. 19457268
Xavier B.B., Miao V.P., Jónsson Z.O., and Andrésson Ó.S. (2012). Mitochondrial genomes from the lichenized fungi Peltigera membranacea and Peltigera malacea: features and phylogeny. Fungal Biology 116(7): 802-814. 22749167
Zhu S., Cao Y.Z., Jiang C., Tan B.Y., Wang Z., Feng S., Zhang L. Su X.H., Brejova B., Vinar T., Xu M., Wang M.X., Zhang S.G., Huang M.R., Wu R. and Zhou Y. (2012). Sequencing the genome of Marssonina brunnea reveals fungus-poplar co-evolution. BMC Genomics 13: 382. 22876864
Zivanovic Y., Wincker P., Vacherie B., Bolotin-Fukuhara M. and Fukuhara H. (2005). Complete nucleotide sequence of the mitochondrial DNA from Kluyveromyces lactis.   FEMS Yeast Research 5: 315-322. 15691736

 

Table 2: Selected articles using mt genomes and mt genes for barcoding, species identification and typing.

Article Information Pubmed ID
Damon C., Barroso G., Férandon C., Ranger J., Fraissinet-Tachet L., Marmeisse R. (2010). Performance of the COX1 gene as a marker for the study of metabolically active Pezizomycotina and Agaricomycetes fungal communities from the analysis of soil RNA. FEMS Microbiol. Ecol. 74: 693-705.  20977493
Dai Y.C., Wang Z., Binder M. and Hibbett D.S. (2006). Phylogeny and a new species of Sparassis (Polyporales, Basidiomycota): evidence from mitochondrial atp6, nuclear rDNA and rpb2 genes. Mycologia 98: 584-592. 17139851
Dentinger B.T., Didukh M.Y. and Moncalvo J.M. (2011). Comparing COI and ITS as DNA barcode markers for mushrooms and allies (Agaricomycotina). PLoS One 6(9): e25081.  21966418
Dupuis J.R., Roe A.D., Sperling F.A. (2012). Multi-locus species delimitation in closely related animals and fungi: one marker is not enough. Molecular Ecology 21(18): 4422-4436.  22891635
Feau N., Vialle A., Allaire M., Maier W. and Hamelin R.C. (2011). DNA barcoding in the rust genus Chrysomyxa and its implications for the phylogeny of the genus. Mycologia 103(6): 1250-1266. 21659458
Férandon C., Moukha S., Callac P., Benedetto J.P., Castroviejo M., Barroso G. (2010). The Agaricus bisporus cox1 gene: the longest mitochondrial gene and the largest reservoir of mitochondrial group I introns. PLoS One 5: e14048. 21124976
Férandon C., Xu J. and Barroso G. (2013). The 135 kbp mitochondrial genome of Agaricus bisporus is the largest known eukaryotic reservoir of group I introns and plasmid-related sequences. Fungal Genet. Biol. 55: 85-91.  23428625
Gao R. and Zhang G. (2013). Potential of DNA barcoding for detecting quarantine fungi. Phytopathology 23718836
Garcia C., La Guerche S., Mouhamadou B., Férandon C., Labarère J., Blancard D., Darriet P. and Barroso G. (2006). A CAPS test allowing a rapid distinction of Penicillium expansum among fungal species collected on grape berries, inferred from the sequence and secondary structure of the mitochondrial SSU-rRNA. Int. J. Food Microbiol. 111: 183-190. 16935376
Ghikas D.V., Kouvelis V.N. and Typas M.A. (2006). 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, while intergenic regions show variation. Archives of Microbiology 185: 393-401.  16552580
Ghikas D.V., Kouvelis V.N. and Typas M.A. (2010). Phylogenetic and biogeographic implications inferred by mitochondrial intergenic region analyses and ITS1-5.8S-ITS2 of the entomopathogenic fungi Beauveria bassiana and B. brongniartii. BMC Microbiology 10: 174.  20553589
Hafez M. and Hausner G. (2011). The highly variable mitochondrial small-subunit ribosomal RNA gene of Ophiostoma minus. Fungal Biol. 115: 1122-1137.  22036291
Hegedus D.D., Khachatourians G.G. (1993). Identification of molecular variants in mitochondrial DNAs of members of the genera Beauveria, Verticillium, Paecilomyces, Tolypocladium and Metarhizium. Applied and Environmental Microbiology  59: 4283-4288. 16349124
Kouvelis V.N., Ghikas D.V., Edgington S., Typas M.A., and Moore D. (2008). Molecular characterisation of isolates of Beauveria bassiana obtained from overwintering and summer populations of Sunn Pest (Eurygaster integriceps). Letters in Applied Microbiology 46: 414-420. 18290810
Kouvelis V.N., Sialakouma A. and Typas M.A. (2008). Mitochondrial gene sequences alone or combined with ITS region sequences provide firm molecular criteria for the classification of Lecanicillium species. Mycological Research 112: 829-844.  18501578
Mahfooz S., Singh P., Maurya D.K., Yadav M.C., Tahoor A., Sahay H., Srivastava A., Prakash A. (2013). Microsatellite repeat dynamics in mitochondrial genomes of phytopathogenic fungi: frequency and distribution in the genic and intergenic regions. Bioinformation 8: 1171-1175. 23275715
Martin F.N. (2010). Mitochondrial haplotype analysis as a tool for differentiating isolates of Verticillium dahliae. Phytopathology 100: 1231-1239. 20932168
Min X.J. and Hickey D.A. (2007). Assessing the effect of varying sequence length on DNA barcoding of fungi. Molecular Ecology Notes 7(3): 365-373. 18784789
Mouhamadou B., Carriconde F., Gryta H., Jargeat P., Manzi S. and Gardes M. (2008). Molecular evolution of mitochondrial ribosomal DNA in the fungal genus Tricholoma: barcoding implications. Fungal Genetics and Biology 45(9): 1219-1226. 18647655
Mouhamadou B., Férandon C., Barroso G. and Labarère J. (2006). The mitochondrial apocytochrome b genes of two Agrocybe species suggest lateral transfers of group I homing introns among phylogenetically distant fungi. Fungal Genet. Biol. 43: 135-145. 16504553
Mullineux S.T., Willows K. and Hausner G. (2011). Evolutionary dynamics of the mS952 intron: a novel mitochondrial group II intron encoding a LAGLIDADG homing endonuclease gene. J. Mol. Evol. 72: 433-449. 21479820
Pantou M.P., Kouvelis V.N. and Typas M.A. (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: 125-136.  16733756
Pramateftaki P.V., Kouvelis V.N., Lanaridis P. and Typas M.A. (2008). Complete mitochondrial genome sequence of the wine yeast Candida zemplinina: intraspecies distribution of a novel group-IIB1 intron with eubacterial affiliations. FEMS Yeast Research 8: 311-327.  18081838
Santamaria M., Vicario S., Pappadà G., Scioscia G., Scazzocchio C. and Saccone C. (2009). Towards barcode markers in Fungi: an intron map of Ascomycota mitochondria. BMC Bioinformatics 10 Suppl 6: S15.  19534740
Seifert K.A. (2009). Progress towards DNA barcoding of fungi. Molecular Ecology Resources 9 Suppl s1: 83-89.  21564968
Seifert K.A., Samson R.A., Dewaard J.R., Houbraken J., Lévesque C.A., Moncalvo J.M., Louis-Seize G. and Hebert P.D. (2007). Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case. Proceedings of the National Academy of Sciences U.S.A. 104(10): 3901-3906. 17360450
Sheen J., Kho Y.H. and Bae K.S. (1993). Genomic sequence of mitochondrial genes coding for ATPase subunit 6 and small subunit ribosomal RNA from Penicillium chrysogenum: a key for molecular systematics on fungi. Nucleic Acids Res. 21 (18), 4393 (1993) 8414999
Sosa-Gomez D.R., Humber R.A., Hodge K.T., Binnek E., Silva-Brandao K.L. (2009). Variability of the mitochondrial ssu rDNA of Nomurea species and
other entomopathogenic fungi from Hypocreales. Mycopathologia 167: 145-154.
18830688
Torriani S.F., Brunner P.C. and McDonald B.A. (2011). Evolutionary history of the mitochondrial genome in Mycosphaerella populations infecting bread wheat, durum wheat and wild grasses. Molecular Phylogenetics and Evolution 58(2): 192-197.  21145978
Uribe D., Khachatourians G.G. (2004). Restriction fragment length polymorphisms of mitochondrial genome of the entomopathogenic fungus Beauveria bassiana reveals high intraspecific variation. Mycological Research 108:1070-1078. 15506018
Valach M., Farkas Z., Fricova D., Kovac J., Brejova B., Vinar T., Pfeiffer I., Kucsera J., Tomaska L., Lang B.F. and Nosek J. (2011). Evolution of linear chromosomes and multipartite genomes in yeast mitochondria. Nucleic Acids Research 39(10): 4202-4219. 21266473
Valach M., Pryszcz L.P., Tomaska L., Gacser A., Gabaldón T. and Nosek J. (2012). Mitochondrial genome variability within the Candida parapsilosis species complex. Mitochondrion 12: 514-519. 22824459

 

Table 3: Selected articles using mt genomes for phylogenetic and evolutionary analyses.

Article Information Pubmed ID
Bietenhader M., Martos A., Tetaud E., Aiyar R.S., Sellem C.H., Kucharczyk R., Clauder-Münster S., Giraud M.F., Godard F., Salin B., Sagot I., Gagneur J., Déquard-Chablat M., Contamine V., Hermann-Le Denmat S., Sainsard-Chanet A., Steinmetz L.M., di Rago J.P. (2012). Experimental relocation of the mitochondrial ATP9 gene to the nucleus reveals forces underlying mitochondrial genome evolution. PLoS Genetics 8(8): e1002876.  22916027
Binder M., Hibbett D.S. (2006). Molecular systematics and biological diversification of Boletales. Mycologia 98: 971-981. 17486973
Bullerwell C.E. and Lang B.F. (2005). Fungal evolution: the case of the vanishing mitochondrion. Current Opinion in Microbiology 8(4): 362-369. 15993645
Burger G., Gray M.W. and Lang B.F. (2003). Mitochondrial genomes: anything goes. Trends in Genetics 19(12): 709-716.  14642752
Castellana S., Vicario S. and Saccone C. (2011). Evolutionary patterns of the mitochondrial genome in Metazoa: exploring the role of mutation and selection in mitochondrial protein coding genes. Genome Biology and Evolution  3: 1067-1079 21551352
Clark-Walker G.D. (1992).  Evolution of mitochondrial genomes in fungi. In "Mitochondrial Genomes" (Eds: Welstenholme D.R., Jeon K.W.) San Diego,
Academic Press, pp. 89-127.
N/A
Dentinger B.T., Ammirati J.F., Both E.E., Desjardin D.E., Halling R.E., Henkel T.W., Moreau P.A., Nagasawa E., Soytong K., Taylor A.F., Watling R., Moncalvo J.M. and McLaughlin D.J. (2010). Molecular phylogenetics of porcini mushrooms (Boletus section Boletus). Mol. Phylogenet. Evol. 57: 1276-1292. 20970511
Ghikas D.V., Kouvelis V.N. and Typas M.A. (2006). 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, while intergenic regions show variation. Archives of Microbiology 185: 393-401.  16552580
Gray M.W., Burger G. and Lang B.F. (1999). Mitochondrial evolution. Science 283(5407): 1476-1481.  10066161
Gray M.W., Burger G. and Lang B.F. (2001). The origin and early evolution of mitochondria. Genome Biology 2(6): REVIEWS1018. 11423013
Kouvelis V.N., Ghikas D.V. and Typas M.A. (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: 930-940. 15341915
Lang B.F., Gray M.W. and Burger G. (1999). Mitochondrial genome evolution and the origin of eukaryotes. Annual Review of Genetics 33: 351-397. 10690412
Lang B.F., Seif E., Gray M.W., O'Kelly C.J. and Burger G. (1999). A comparative genomics approach to the evolution of eukaryotes and their mitochondria. Journal of Eukaryotic Microbiology 46(4): 320-326. 10461380
Lipinski K.A., Kaniak-Golik A. and Golik P. (2010). Maintenance and expression of the S. cerevisiae mitochondrial genome-from genetics to evolution and systems biology. Biochimica and Biophysica Acta 1797(6-7): 1086-1098.  20056105
Liu Y., Leigh J.W., Brinkmann H., Cushion M.T., Rodriguez-Ezpeleta N., Philippe H., Lang B.F. (2009). Phylogenomic analyses support the monophyly of Taphrinomycotina, including Schizosaccharomyces fission yeasts. Molecular Biology and Evolution 26(1): 27-34. 18922765
Liu Y., Steenkamp E.T., Brinkmann H., Forget L., Philippe H. and Lang B.F. (2009). Phylogenomic analyses predict sistergroup relationship of nucleariids and fungi and paraphyly of zygomycetes with significant support. BMC Evolutionary  Biology 9: 272.  19939264
Pantou M.P., Kouvelis V.N. and Typas M.A. (2008). The complete mitochondrial genome of Fusarium oxysporum: insights into fungal mitochondrial evolution. Gene 419: 7-15  18538510
Paquin B., Laforest M.J., Forget L., Roewer I., Wang Z., Longcore J. and Lang B.F. (1997). The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression. Current Genetics 31(5): 380-395. 9162109
Pramateftaki P.V., Kouvelis V.N., Lanaridis P. and Typas M.A. (2006). The mitochondrial genome of the wine yeast Hanseniaspora uvarum: a unique genome organization among yeast/fungal counterparts. FEMS Yeast Research 6: 77-90.  16423073
Rivas Plata E. and Lumbsch H.T. (2011).Parallel evolution and phenotypic divergence in lichenized fungi: a case study in the lichen-forming fungal family Graphidaceae (Ascomycota: Lecanoromycetes: Ostropales). Mol. Phylogenet. Evol. 61: 45-63.  21605691
Sankoff D., Bryant D., Deneault M., Lang B.F. and Burger G. (2000). Early eukaryote evolution based on mitochondrial gene order breakpoints. Journal of Computational Biology 7(3-4): 521-535. 11108477
van de Sande W.W.J. (2012). Phylogenetic analysis of the complete mitochondrial genome of Madurella mycetomatis confirms its taxonomic position within the order Sordariales. PLoS ONE 7: e38654.  22701687
Xavier B.B., Miao V.P., Jónsson Z.O., and Andrésson Ó.S. (2012). Mitochondrial genomes from the lichenized fungi Peltigera membranacea and Peltigera malacea: features and phylogeny. Fungal Biology 116(7): 802-814. 22749167


Contact:
The MitoFun Team welcomes suggestions, comments and submission of novel fungal mt genomes. Please feel free to contact any of the MitoFun Team Members.

Acknowledgements:
MitoFun is a collaborative project between the Department of Genetics and Biotechnology (Faculty of Biology, University of Athens) and the Bioinformatics Research Laboratory (Department of Biological Sciences, University of Cyprus).
This project was partially funded by the University of Athens (Kapodistrias grant no. 70/4/8804) and the University of Cyprus (Grant 3/311).
The MitoFun development team: Ioannis Kirmitzoglou, Maria Ntertili, Stella Tamana, Ioanna Kalvari, Michalis Vasiliadis, Vassili N. Kouvelis, Vasilis J. Promponas, and Milton A. Typas
© 2006-2013 Bioinformatics Research Laboratory, University of Cyprus
© 2006-2013 Department of Genetics and Biotechnology, University of Athens