The current status of species recognition and identification in Aspergillus

Bachtrog, 2006, Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group, Evolution, 60, 292, 10.1111/j.0014-3820.2006.tb01107.x Balajee, 2005, Aspergillus lentulus sp. nov., a new sibling species of A. fumigatus, Eukaryotic Cell, 4, 625, 10.1128/EC.4.3.625-632.2005 Bensasson, 2001, Mitochondrial pseudogenes: evolution” s misplaced witnesses, Trends in Ecology and Evolution, 16, 314, 10.1016/S0169-5347(01)02151-6 Berbee, 1995, Is Penicillium monophyletic? An evaluation of phylogeny in the family Trichocomaceae from 18S, 5.8S and ITS ribosomal DNA sequence data, Mycologia, 87, 210, 10.2307/3760907 Bhadury, 2006, Development and evaluation of a DNA-barcoding approach for the rapid identification of nematodes, Marine Ecology, 320, 1, 10.3354/meps320001 Bruns, 2001, ITS Reality, Inoculum, 52, 2 Chase, 2005, Land plants and DNA barcodes: short-term and long-term goals, Philosophical Transactions of the Royal Society of London B: Biological Sciences, 360, 1889, 10.1098/rstb.2005.1720 Chu, 2006, Ribosomal RNA as molecular barcodes: a simple correlation analysis without sequence alignment, Bioinformatics, 22, 1690, 10.1093/bioinformatics/btl146 DeSalle, 2005, The unholy trinity, taxonomy, species delimitation and DNA barcoding, Proceedings of the Royal Society of London B: Biological Sciences, 360, 1905, 10.1098/rstb.2005.1722 Desnos-Ollivier, 2006, Molecular identification of black-grain mycetoma agents, Journal of Clinical Microbiology, 44, 3517, 10.1128/JCM.00862-06 Dettman, 2006, Multilocus sequence data reveal extensive phylogenetic species diversity within the Neurospora discreta complex, Mycologia, 98, 436, 10.3852/mycologia.98.3.436 van Diepeningen, 1997, Heterokaryon incompatibility blocks virus transfer among natural isolates of black aspergilli, Current Genetics, 32, 209, 10.1007/s002940050268 Dobzhansky, 1951 Druzhinina, 2005, An oligonucleotide barcode for species identification in Trichoderma and Hypocrea, Fungal Genetics and Biology, 42, 813, 10.1016/j.fgb.2005.06.007 Dyer, 2005, Reproduction in Aspergillus fumigatus: sexuality in a supposedly asexual species?, Medical Mycology, 43, S7, 10.1080/13693780400029015 Dykhuizen, 1991, Recombination in Escherichia coli and the definition of biological species, Journal of Bacteriology, 173, 7257, 10.1128/jb.173.22.7257-7268.1991 Earl, 1981, High frequency transfer of species specific mitochondrial DNA sequences between members of the Aspergillaceae, Current Genetics, 3, 221, 10.1007/BF00429824 Fisher, 2002, Molecular and phenotypic description of Coccidioides posadasii sp. nov., previously recognized as the non-California population of Coccidioides immitis, Mycologia, 94, 73, 10.2307/3761847 Frisvad, 2000, Neopetromyces gen. nov. and an overview of teleomorphs of Aspergillus subgenus Circumdati, Studies in Mycology, 45, 201 Frisvad, 2005, Taxonomic comparison of three different groups of aflatoxin producers and a new efficient producer of aflatoxin B1, sterigmatocystin and 2-O-methylsterigmatocystin, Aspergillus rambellii sp. nov., Systematic and Applied Microbiology, 28, 442, 10.1016/j.syapm.2005.02.012 Gams, 1985, Infrageneric taxa of Aspergillus, 55 Geiser, 2004, Practical molecular taxonomy of fungi, 1 Geiser, 2000, The phylogenetics of mycotoxin and sclerotium production in Aspergillus flavus and Aspergillus oryzae, Fungal Genetics and Biology, 31, 169, 10.1006/fgbi.2000.1215 Geiser, 2004, FU.S.A.RIUM-ID v. 1.0: A DNA sequence database for identifying Fusarium, European Journal of Plant Pathology, 110, 473, 10.1023/B:EJPP.0000032386.75915.a0 Geiser, 1998, Cryptic speciation and recombination in the aflatoxin-producing fungus Aspergillus flavus, Proceedings of the National Academy of Sciences U.S.A., 95, 388, 10.1073/pnas.95.1.388 Geiser, 1996, Loss of meiosis in Aspergillus, Molecular Biology and Evolution, 13, 809, 10.1093/oxfordjournals.molbev.a025641 Gielkens, 1997, Arabinoxylan degradation by fungi: characterization of the arabinoxylan-arabinofuranohydrolase encoding genes from Aspergillus niger and Aspergillus tubingensis, Current Genetics, 31, 22, 10.1007/s002940050172 Hajibabaei, 2006, DNA barcodes distinguish species of tropical Lepidoptera, Proceedings of the National Academy of Sciences U.S.A., 103, 968, 10.1073/pnas.0510466103 Hamari, 2001, Intron mobility results in rearrangement in mitochondrial DNAs of heterokaryon incompatible Aspergillus japonicus strains after protoplast fusion, Fungal Genetics and Biology, 33, 83, 10.1006/fgbi.2001.1272 Hamari, 1997, Molecular and phenotypic characterization of Aspergillus japonicus and Aspergillus aculeatus strains with special regard to their mitochondrial DNA polymorphisms, Antonie Van Leeuwenhoek, 72, 337, 10.1023/A:1000578913759 Hamari, 2003, Interpretation of intraspecific variability in mtDNAs of Aspergillus niger strains and rearrangement of their mtDNAs following mitochondrial transmissions, FEMS Microbiology Letters, 221, 63, 10.1016/S0378-1097(03)00165-4 Hebert, 2004, Ten species in one, DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator, Proceedings of the National Academy of Sciences U.S.A., 101, 14812, 10.1073/pnas.0406166101 Hebert, 2003, Barcoding animal life: cytochrome C oxidase subunit 1 divergences among closely related species, Proceedings of the Royal Society of London B: Biological Sciences, 270, S96, 10.1098/rsbl.2003.0025 Hebert, 2004, Identification of birds through DNA barcodes, PLoS Biology, 2, e312, 10.1371/journal.pbio.0020312 Hey, 2001 Hickerson, 2006, DNA barcoding will often fail to discover new animal species over broad parameter space, Systematic Biology, 55, 729, 10.1080/10635150600969898 Hillis, 1993, An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis, Systematic Biology, 42, 182, 10.1093/sysbio/42.2.182 Hong, 2005, Polyhphasic taxonomy of Aspergillus fumigatus and related species, Mycologia, 97, 1316, 10.3852/mycologia.97.6.1316 Hurst, 2005, Problems with mitochondrial DNA as a marker in population, phylogeographic and phylogenetic studies: the effects of inherited symbionts, Proceedings of the Royal Society B. Biological Sciences, 272, 1525, 10.1098/rspb.2005.3056 Johannesson, 2004, Positive directional selection in the proline-rich antigen (PRA) gene among the human pathogenic fungi Coccidioides immitis, C. posadasii and their closest relatives, Molecular Biology and Evolution, 21, 1134, 10.1093/molbev/msh124 Juhász, 2007, Interpretation of mtDNA RFLP variability among Aspergillus tubingensis isolates, Antonie van Leeuwenhoek, 91, 209, 10.1007/s10482-006-9110-x Juhász, 2004, Mitochondrial DNA organisation of the mtDNA type 2b of Aspergillus tubingensis compared to the Aspergillus niger mtDNA type 1a, FEMS Microbiology Letters, 241, 119, 10.1016/j.femsle.2004.10.025 Kevei, 1996, Molecular polymorphism and phenotypic variation in Aspergillus carbonarius, Antonie Van Leeuwenhoek, 70, 59, 10.1007/BF00393570 Kevei, 1997, Recombination of mitochondrial DNAs following transmission of mitochondria among incompatible strains of black aspergilli, Molecular and General Genetics, 254, 379, 10.1007/s004380050430 Kimura, 1980, A simple method for estimating evolutionary rate of base substitutions through comparative studies on nucleotide sequences, Journal of Molecular Evolution, 2, 87, 10.1007/BF01653945 Klich, 2001, A new sterigmatocystin-producing Emericella variant from agricultural desert soils, Systematic and Applied Microbiology, 24, 131, 10.1078/0723-2020-00007 Koufopanou, 1997, Concordance of gene genealogies reveals reproductive isolation in the pathogenic fungus Coccidioides immitis, Proceedings of the National Academy of Sciences U.S.A., 94, 5478, 10.1073/pnas.94.10.5478 Kress, 2007, A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnHpsbA spacer region, PLoS ONE, 2, e508, 10.1371/journal.pone.0000508 Kress, 2005, Use of DNA barcodes to identify flowering plants, Proceedings of the National Academy of Sciences U.S.A., 102, 8369, 10.1073/pnas.0503123102 Kumar, 2004, MEGA 3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment, Briefings in Bioinformatics, 5, 150, 10.1093/bib/5.2.150 Litaker, 2007, Recognizing Dinoflagellate species using its rDNA sequences, Journal of Phycology, 43, 344, 10.1111/j.1529-8817.2007.00320.x Little, 2007, A comparison of algorithms for the identification of specimens using DNA barcodes: examples from gymnosperms, Cladistics, 23, 1, 10.1111/j.1096-0031.2006.00126.x Maslov, 2007, Discovery and barcoding by analysis of spliced leader RNA gene sequences of new isolates of Trypanosomatidae from Heteroptera in Costa Rica and Ecuador, Journal of Eukaryotic Microbiology, 54, 57, 10.1111/j.1550-7408.2006.00150.x Min, 2007, Assessing the effect of varying sequence length on DNA barcoding of fungi, Molecular Ecology Notes, 7, 365, 10.1111/j.1471-8286.2007.01698.x Moritz, 2004, DNA barcoding: promise and pitfalls, PLoS Biology, 2, e354, 10.1371/journal.pbio.0020354 Nierman, 2006, Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus, Nature, 439, 502, 10.1038/nature04572 O'Donnell, 2000, Molecular phylogeny of the Nectria haematococca-Fusarium solani species complex, Mycologia, 92, 919, 10.2307/3761588 O'Donnell, 1998, Molecular systematics and phylogeography of the Gibberella fujikuroi species complex, Mycologia, 90, 465, 10.2307/3761407 O'Donnell, 2004, Genealogical concordance between the mating type locus and seven other nuclear genes supports formal recognition of nine phylogenetically distinct species within the Fusarium graminearum clade, Fungal Genetics and Biology, 41, 600, 10.1016/j.fgb.2004.03.003 Ogawa, 2000, Evolutionary relationships of the cleistothecial genera with Penicillium, Geosmithia, Merimbla and Sarophorum anamorphs as inferred from 18S rDNA sequence divergence, 149 Paoletti, 2005, Evidence for sexuality in the opportunistic fungal pathogen Aspergillus fumigatus, Current Biology, 15, 1242, 10.1016/j.cub.2005.05.045 Parenicova, 2001, Combined molecular and biochemical approach identifies Aspergillus japonicus and Aspergillus aculeatus as two species, Applied and Environmental Microbiology, 67, 521, 10.1128/AEM.67.2.521-527.2001 Park, 2007, Identification of genes suitable for DNA barcoding of morphologically indistinguishable korean halichondriidae sponges, Molecules and Cells, 23, 220 Peterson, 1995, Phylogenetic analysis of Aspergillus Sections Cremei and Wentii, based on ribosomal DNA sequences, Mycological Research, 99, 1349, 10.1016/S0953-7562(09)81220-3 Peterson, 2000, Phylogenetic relationships in Aspergillus based on rDNA sequence analysis, 323 Pitt, 2000, List of accepted species and their teleomorphs in the family Trichocomaceae, 9 Pringle, 2005, Cryptic speciation in the cosmopolitan and clonal human pathogenic fungus Aspergillus fumigatus, Evolution, 59, 1886, 10.1111/j.0014-3820.2005.tb01059.x Raper, 1965 Rokas, 2003, Genome-scale approaches to resolving incongruence in molecular phylogenies, Nature, 425, 798, 10.1038/nature02053 Rydholm, 2007, DNA sequence characterization and molecular evolution of MAT1 and MAT2 mating-type loci of the self-compatible ascomycete mold Neosartorya fischeri, Eukaryotic Cell, 6, 868, 10.1128/EC.00319-06 Samson, 2000, List of names of Trichocomaceae published between 1992 and 1999, 73 Samson, 1985, Typification of the species of Aspergillus and associated teleomorphs, 143 Samson, 2006, Old and new concepts of species differentiation in Aspergillus, Medical Mycology, 44, S133, 10.1080/13693780600913224 Samson, 2004, New ochratoxin or sclerotium producing species in Aspergillus section Nigri, Studies in Mycology, 50, 45 Saunders, 2005, Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications, Philosophical Transactions of the Royal Society of London B: Biological Sciences, 360, 1879, 10.1098/rstb.2005.1719 Schill, 2007, Identification and differentiation of Heterotardigrada and Eutardigrada species by riboprinting, Journal of Zoological Systematics and Evolutionary Research, 45, 184, 10.1111/j.1439-0469.2007.00409.x Schwarz, 2006, Molecular identification of Zygomycetes from culture and experimentally infected tissues, Journal of Clinical Microbiology, 44, 340, 10.1128/JCM.44.2.340-349.2006 Scicluna, 2006, DNA barcoding of Blastocystis, Protist, 157, 77, 10.1016/j.protis.2005.12.001 Seifert, 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, 3901, 10.1073/pnas.0611691104 Sonnenberg, 2007, An evaluation of LSU rDNA D1-D2 sequences for their use in species identification, Frontiers in Zoology, 4, 6, 10.1186/1742-9994-4-6 Strugnell, 2007, A barcode of life database for Cephalopoda? Considerations and concerns, Reviews in Fish Biology and Fisheries, 17, 337, 10.1007/s11160-007-9043-0 Summerbell, 2007, ITS barcodes for Trichophyton tonsurans and T. equinum, Medical Mycology, 45, 193, 10.1080/13693780601087614 Swofford, 2003 Sword, 2007, Double trouble fort grasshopper molecular systematics: infra-individual heterogeneity of both mitochondrial 12S-valine-16S and nuclear internal transcribed spacer ribosomal RNA sequences in Hesperotettix viridis (Orthoptera: Acrididae), Systematic Entomology, 32, 420, 10.1111/j.1365-3113.2007.00385.x Taylor, 2000, Phylogenetic species recognition and species concepts in fungi, Fungal Genetics and Biology, 31, 21, 10.1006/fgbi.2000.1228 Taylor, 2006, Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi, Philosophical Transactions of the Royal Society B-Biological Sciences, 361, 1947, 10.1098/rstb.2006.1923 Thalmann, 2004, Unreliable mtDNA data due to nuclear insertions: A cautionary tale from analysis of humans and other great apes, Molecular Ecology, 13, 321, 10.1046/j.1365-294X.2003.02070.x Thom, 1926 Thom, 1945 Tóth, 1998, Recombination of mitochondrial DNA without selection pressure among compatible strains of the Aspergillus niger species aggregate, Current Genetics, 33, 199, 10.1007/s002940050327 Townsend, 2007, Profiling phylogenetic informativeness, Systematic Biology, 56, 222, 10.1080/10635150701311362 Varga, 1993, Restriction fragment length polymorphisms in the mitochondrial DNAs of the Aspergillus niger aggregate, Mycological Research, 97, 1207, 10.1016/S0953-7562(09)81286-0 Varga, 1994, Mitochondrial DNA restriction fragment length polymorphisms in field isolates of the Aspergillus niger aggregate, Canadian Journal of Microbiology, 40, 612, 10.1139/m94-098 Varga, 2007, Aspergillus brasiliensis sp. nov., a biseriate black Aspergillus species with world-wide distribution, International Journal of Systematic and Evolutionary Microbiology, 57, 1925, 10.1099/ijs.0.65021-0 de Vries, 2005, Aspergillus vadensis, a new species of the group black aspergilli, Antonie van Leeuwenhoek, 87, 195, 10.1007/s10482-004-3194-y Wang, 2000, Mitochondrial cytochrome b gene analysis of Aspergillus fumigatus and related species, Journal of Clinical Microbiology, 38, 1352, 10.1128/JCM.38.4.1352-1358.2000 Ward, 2005, DNA barcoding Australia” s fish species, Proceedings of the Royal Society of London B: Biological Sciences, 360, 1847, 10.1098/rstb.2005.1716 Wiemers, 2007, Does the DNA barcoding gap exist?, Frontiers in Zoology, 4, 8, 10.1186/1742-9994-4-8 Wiens, 2002, Delimiting species limits in spiny lizards (Sceloporus), Systematic Biology, 51, 69, 10.1080/106351502753475880 Witiak SM, Samson RA, Varga J, Rokas A, Geiser DM (2007). Phylogenetic markers for the genus Aspergillus developed from complete genome sequences. 24th Fungal Genetics Conference, Asilomar, Abstract No. 130. Abliz, 2001, New and interesting species of Eurotium from Chinese soil, Mycoscience, 42, 289, 10.1007/BF02463921 Dasmahapatra, 2006, DNA barcodes: recent successes and future prospects, Heredity, 97, 254, 10.1038/sj.hdy.6800858 Frisvad, 2004, New ochratoxin A producing species of Aspergillus section Cirumdati, Studies in Mycology, 50, 23 Frisvad, 2004, Emericella venezuelensis, a new species with stellate ascospores producing sterigmatocystin and aflatoxin B1, Systematic and Applied Microbiology, 27, 672, 10.1078/0723202042369910 Hong, 2006, Novel Neosartorya species isolated from soil in Korea, International Journal of Systematic and Evolutionary Microbiology, 56, 477, 10.1099/ijs.0.63980-0 Hong, 2007, New taxa of Neosartorya and Aspergillus in Aspergillus section Fumigati, Antonie van Leeuwenhoek Horie, 2003, Two new species of Neosartorya from Amazonian soil, Brazil, Mycoscience, 44, 397, 10.1007/S10267-003-0132-1 Horie, 2001, Neosartorya takakii, a new species from soil in Brazil, Mycoscience, 42, 91, 10.1007/BF02463980 Horie, 2000, Emericella qinquxianii, a new species from desert soil in China, Mycoscience, 41, 183, 10.1007/BF02464329 Ito, 2001, Aspergillus pseudotamarii, a new aflatoxin producing species in Aspergillus section Flavi, Mycological Research, 105, 233, 10.1017/S0953756200003385 Noonim, 2007, Two novel species of Aspergillus section Nigri from Thai coffee beans, International Journal of Systematic and Evolutionary Microbiology Perrone, 2007, Aspergillus uvarum sp. nov., an uniseriate black Aspergillus species isolated from grapes in Europe, International Journal of Systematic and Evolutionary Microbiology Peterson, 2001, Aspergillus bombycis, a new aflatoxigenic species and genetic variation in its sibling species, A. nomius, Mycologia, 93, 689, 10.2307/3761823 Pildain, 2007, Two new aflatoxin producing Aspergillus species from Argentinean peanuts, International Journal of Systematic and Evolutionary Microbiology Samson, 2007, Polyphasic taxonomy of Aspergillus section Fumigati and its teleomoorph Neosartorya, Studies in Mycology, 59, 147, 10.3114/sim.2007.59.14 Serra, 2006, Aspergillus ibericus: a new species of section Nigri isolated from grapes, Mycologia, 98, 295, 10.3852/mycologia.98.2.295 Takada, 2001, Two new heterothallic Neosartorya from African soil, Mycoscience, 42, 361, 10.1007/BF02461219 Vences, 2005, Deciphering amphibian diversity through DNA barcoding: chances and challenges, Philosophical Transactions of the Royal Society B: Biological Sciences, 360, 1859, 10.1098/rstb.2005.1717 Vences, 2005, Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians, Frontiers in Zoology, 2, 5, 10.1186/1742-9994-2-5 Whitworth, 2007, DNA barcoding cannot reliably identify species of the blowfly genus Protocalliphora (Diptera: Calliphoridae), Proceedings of the Royal Society of London B: Biological Sciences, 274, 1731, 10.1098/rspb.2007.0062 Zotti, 2002, Aspergillus persii: A new species in section Circumdati, Mycotaxon, 83, 269