β-tubulin paralogue tubC is frequently misidentified as the benA gene in Aspergillus section Nigri taxonomy: Primer specificity testing and taxonomic consequences

Persoonia: Molecular Phylogeny and Evolution of Fungi

Volumn 29, Issue , 2012, Pages 1-10

  Hubka, V ^a,b   Kolarik, M ^a,b  

^a INSTITUTE OF MICROBIOLOGY   (Czech Republic)

^b CHARLES UNIVERSITY   (Czech Republic)

Author keywords

Biseriate black aspergilli; Codon usage; Gene duplication; Incongruent trees; Paralogous genes; PCR fingerprinting; Primer design; Uniseriate black aspergilli

Indexed keywords

ASPERGILLUS; ASPERGILLUS ACULEATUS; ASPERGILLUS JAPONICUS;

EID: 84872503635     PISSN: 00315850     EISSN: None     Source Type: Journal    
DOI: 10.3767/003158512X658123     Document Type: Article

References (57)

1. Andersen MR, Salazar MP, Schaap PJ, Vondervoort PJI van de, Culley D, et al. 2011. Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88. Genome Research 21: 885-897.
2. Arabatzis M, Kambouris M, Kyprianou M, Chrysaki A, Foustoukou M, et al. 2011. Polyphasic identification and susceptibility to seven antifungals of 102 Aspergillus isolates recovered from immunocompromised hosts in Greece. Antimicrobial Agents and Chemotherapy 55: 3025-3030.
3. Askenazi M, Driggers EM, Holtzman DA, Norman TC, Iverson S, et al. 2003. Integrating transcriptional and metabolite profiles to direct the engineering of lovastatin-producing fungal strains. Nature Biotechnology 21: 150-156.
4. Batista AC, Maia HdS. 1955. Alguns Aspergillales de contaminação. Anais da Sociedade de Biologia de Pernambuco 13: 91-100.
5. Bennetzen JL, Hall BD. 1982. Codon selection in yeast. Journal of Biological Chemistry 257: 3026-3031.
6. Dutcher SK. 2001. The tubulin fraternity: alpha to eta. Current Opinion in Cell Biology 13: 49-54.
7. Einax E, Voigt K. 2003. Oligonucleotide primers for the universal amplification of β-tubulin genes facilitate phylogenetic analyses in the regnum fungi. Organisms Diversity & Evolution 3: 185-194.
8. Feau N, Decourcelle T, Husson C, Desprez-Loustau M-L, Dutech C. 2011. Finding single copy genes out of sequenced genomes for multilocus phylogenetics in non-model fungi. PLoS One 6: e18803.
9. Ferracin LM, Fier CB, Vieira MLC, Monteiro-Vitorello CB, Varani AM, et al. 2012. Strain-specific polyketide synthase genes of Aspergillus niger. International Journal of Food Microbiology 155: 137-145.
10. Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, et al. 2005. Sequencing of Aspergillus nidulans and comparative analysis with A. fumigates and A. oryzae. Nature 438: 1105-1115.
11. Gardes M, Bruns TD. 1993. ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts. Molecular Ecology 2: 113-118.
12. Glass NL, Donaldson GC. 1995. Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes. Applied and Environmental Microbiology 61: 1323-1330.
13. Hamari Z, Kevei F, Kovács É, Varga J, Kozakiewicz Z, et al. 1997. Molecular and phenotypic characterization of Aspergillus japonicus and Aspergillus aculeatus strains with special regard to their mitochondrial DNA polymorphisms. Antonie van Leeuwenhoek 72: 337-347.
14. Hammer Ø, Harper DAT, Ryan PD. 2001. PAST: paleontological statistics software package for education and data analysis. Palaeontologia Electronica 4: 1-9.
15. Hendrickx M, Beguin H, Detandt M. 2012. Genetic re-identification and antifungal susceptibility testing of Aspergillus section Nigri strains of the BCCM/IHEM collection. Mycoses 55: 148-155.
16. Howard SJ, Harrison E, Bowyer P, Varga J, Denning DW. 2011. Cryptic species and azole resistance in the Aspergillus niger complex. Antimicrobial Agents and Chemotherapy 55: 4802-4809.
17. Hubka V. 2011. β-tubulin paralogs in Aspergillus: taxonomical importance and molecular tools for distinguishing. Master Thesis, Department of Botany, Charles University in Prague, Czech Republic.
18. Huelsenbeck JP, Ronquist F. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
19. Ikemura T. 1981. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system. Journal of Molecular Biology 151: 389-409.
20. Katoh K, Kuma K, Toh H, Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research 33: 511-518.
21. Keeling PJ, Luker MA, Palmer JD. 2000. Evidence from beta-tubulin phylogeny that microsporidia evolved from within the fungi. Molecular Biology and Evolution 17: 23-31.
22. Lavner Y, Kotlar D. 2005. Codon bias as a factor in regulating expression via translation rate in the human genome. Gene 345: 127-138.
23. Lloyd AT, Sharp PM. 1991. Codon usage in Aspergillus nidulans. Molecular and General Genetics 230: 288-294.
24. May GS. 1989. The highly divergent β-tubulins of Aspergillus nidulans are functionally interchangeable. Journal of Cell Biology 109: 2267-2274.
25. May GS, Gambino J, Weatherbee JA, Morris NR. 1985. Identification and functional analysis of beta-tubulin genes by site specific integrative transformation in Aspergillus nidulans. Journal of Cell Biology 101: 712-719.
26. May GS, Tsang MLS, Smith H, Fidel S, Morris NR. 1987. Aspergillus nidulans β-tubulin genes are unusually divergent. Gene 55: 231-243.
27. Meijer M, Houbraken J, Dalhuijsen S, Samson RA, Vries RP de. 2011. Growth and hydrolase profiles can be used as characteristics to distinguish Aspergillus niger and other black aspergilli. Studies in Mycology 69: 19-30.
28. Najafabadi HS, Goodarzi H, Salavati R. 2009. Universal function-specificity of codon usage. Nucleic Acids Research 37: 7014-7023.
29. Noonim P, Mahakarnchanakul W, Varga J, Frisvad JC, Samson RA. 2008. Two novel species of Aspergillus section Nigri from Thai coffee beans. International Journal of Systematic and Evolutionary Microbiology 58: 1727-1734.
30. Nováková A, Hubka V, Saiz-Jimenez C, Kolarik M. 2012. Aspergillus baeticus sp. nov. and Aspergillus thesauricus sp. nov.: two new species in section Usti originating from Spanish caves. International Journal of Systematic and Evolutionary Microbiology doi: 10.1099/ijs.0.041004-0.
31. O'Donnell K. 1992. Ribosomal DNA internal transcribed spacers are highly divergent in the phytopathogenic ascomycete Fusarium sambucinum (Gibberella pulicaris). Current Genetics 22: 213-220.
32. 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: 103-116.
33. Oakley BR, Morris NR. 1980. Nuclear movement is β-tubulin-dependent in Aspergillus nidulans. Cell 19: 255-262.
34. Oakley BR, Morris NR. 1981. A β-tubulin mutation in Aspergillus nidulans that blocks microtubule function without blocking assembly. Cell 24: 837-845.
35. Pařenicová L, Skouboe P, Frisvad J, Samson RA, Rossen L, et al. 2001. Combined molecular and biochemical approach identifies Aspergillus japonicus and Aspergillus aculeatus as two species. Applied and Environmental Microbiology 67: 521-527.
36. Payne GA, Nierman WC, Wortman JR, Pritchard BL, Brown D, et al. 2006. Whole genome comparison of Aspergillus flavus and A. oryzae. Medical Mycology 44: 9-11.
37. Peden JF. 1999. Analysis of codon usage. PhD thesis, Department of Genetics, University of Nottingham, UK.
38. Perrone G, Mule G, Susca A, Battilani P, Pietri A, et al. 2006. Ochratoxin A production and amplified fragment length polymorphism analysis of Aspergillus carbonarius, Aspergillus tubingensis, and Aspergillus niger strains isolated from grapes in Italy. Applied and Environmental Microbiology 72: 680-685.
39. Perrone G, Varga J, Susca A, Frisvad JC, Stea G, et al. 2008. Aspergillus uvarum sp. nov., an uniseriate black Aspergillus species isolated from grapes in Europe. International Journal of Systematic and Evolutionary Microbiology 58: 1032-1039.
40. Peterson SW. 2008. Phylogenetic analysis of Aspergillus species using DNA sequences from four loci. Mycologia 100: 205-226.
41. Raper KB, Fennell DI. 1965. The genus Aspergillus. Williams & Wilkins Co., USA.
42. Samson RA, Houbraken JAMP, Kuijpers AFA, Frank JM, Frisvad JC. 2004. New ochratoxin A or sclerotium producing species in Aspergillus section Nigri. Studies in Mycology 50: 45-61.
43. Samson RA, Noonim P, Meijer M, Houbraken J, Frisvad JC, et al. 2007. Diagnostic tools to identify black aspergilli. Studies in Mycology 59: 129-145.
44. Samson RA, Varga J. 2009. What is a species in Aspergillus? Medical Mycology 47: S13-S20.
45. Sharp PM, Devine KM. 1989. Codon usage and gene expression level in Dictyostelium discoideum: highly expressed genes do "prefer" optimal codons. Nucleic Acids Research 17: 5029-5039.
46. Sharp PM, Tuohy TMF, Mosurski KR. 1986. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Research 14: 5125-5143.
47. Silva DM, Batista LR, Rezende EF, Fungaro MHP, Sartori D, et al. 2011. Identification of fungi of the genus Aspergillus section Nigri using polyphasic taxonomy. Brazilian Journal of Microbiology 42: 761-773.
48. Sørensen A, Lübeck PS, Lübeck M, Nielsen KF, Ahring BK, et al. 2011. Aspergillus saccharolyticus sp. nov., a new black Aspergillus species isolated in Denmark. International Journal of Systematic and Evolutionary Microbiology 61: 3077-3083.
49. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28: 2731-2739.
50. Tuthill DE. 2004. Genetic variation and recombination in Penicillium miczynskii and Eupenicillium species. Mycological Progress 3: 3-12.
51. Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, et al. 2007. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Research 35: W71-W74.
52. Varga J, Frisvad JC, Kocsubé S, Brankovics B, Tóth B, et al. 2011. New and revisited species in Aspergillus section Nigri. Studies in Mycology 69: 1-17.
53. Varga J, Kocsubé S, Tóth B, Frisvad JC, Perrone G, et al. 2007. Aspergillus brasiliensis sp. nov., a biseriate black Aspergillus species with world-wide distribution. International Journal of Systematic and Evolutionary Microbiology 57: 1925-1932.
54. Vries RP de, Frisvad JC, Vondervoort PJI van de, Burgers K, Kuijpers AFA, et al. 2005. Aspergillus vadensis, a new species of the group of black Aspergilli. Antonie van Leeuwenhoek 87: 195-203.
55. Weatherbee JA, May GS, Gambino J, Morris NR. 1985. Involvement of a particular species of beta-tubulin (beta 3) in conidial development in Aspergillus nidulans. Journal of Cell Biology 101: 706-711.
56. Weatherbee JA, Morris NR. 1984. Aspergillus contains multiple tubulin genes. Journal of Biological Chemistry 259: 15452-15459.
57. Wortman JR, Fedorova N, Crabtree J, Joardar V, Maiti R, et al. 2006. Whole genome comparison of the A. fumigatus family. Medical Mycology 44: 3-7.