Phylogenetic analyses of penicillia based on partial calmodulin gene sequences

BioSystems

Volumn 88, Issue 1-2, 2007, Pages 113-126

  Wang, Long ^a,b   Zhuang, Wen Ying ^a  

^a INSTITUTE OF MICROBIOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Cluster analysis; Eupenicillium; Evolution; Penicillium; RSCU; Speciation; Talaromyces

Indexed keywords

CALMODULIN;

CLUSTER ANALYSIS; EVOLUTION; FUNGUS; GENETIC ANALYSIS; PHYLOGENETICS; SPECIATION (BIOLOGY);

AMINO ACID SEQUENCE; ANAMORPH; ARTICLE; CLUSTER ANALYSIS; CODON USAGE; CONTROLLED STUDY; FUNGUS ISOLATION; GENE SEQUENCE; INTRON; NEIGHBOR JOINING METHOD; NONHUMAN; NUCLEOTIDE SEQUENCE; PARSIMONY ANALYSIS; PENICILLIUM; PHYLOGENY; PLANT DEVELOPMENT; TALAROMYCES; TELEOMORPH;

EUPENICILLIUM; PENICILLIUM; TALAROMYCES; TRICHOCOMACEAE;

EID: 33846815081     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2006.04.008     Document Type: Article

References (65)

1. Banke S., and Rosendahl S. Development of genetic markers for population studies of Penicillium spp. In: Samson R.A., and Pitt J.I. (Eds). Integration of Modern Taxonomic Methods for Penicillium and Aspergillus Classification (2000), Harwood Academic Publishers, Amsterdam 199-208
2. Benjamin C.R. Ascocarps of Aspergillus and Penicillium. Mycologia 47 (1955) 669-687
3. Berbee M.L., and Taylor J.W. Fungal molecular evolution: gene trees and geologic time. In: McLaughlin D.J., McLaughlin E.G., and Lemke P.A. (Eds). The Mycota VII Part B. Systemtics and Evolution (2001), Springer-Verlag, Berlin Heidelberg 229-245
4. Berbee M.L., Yoshimura A., Sugiyama J., and Taylor J.W. Is Penicillium monophyletic? An evaluation of phylogeny in the family Trichocomaceae from 18S 5. 8S and ITS ribosomal DNA sequence data. Mycologia 87 (1995) 210-222
5. Boysen M., Skouboe P., Frisvad J., and Rossen L. Reclassification of the Penicillium roqueforti group into three species on the basis of molecular genetic and biochemical profiles. Microbiology 142 (1996) 541-549
6. Carbone I., and Kohn L.M. A method for designing primer sets for speciation studies in filamentous ascomycetes. Mycologia 91 (1999) 553-556
7. Dodge B.O. The perithecium and ascus of Penicillium. Mycologia 25 (1933) 90-104
8. Emmons C.W. The ascocarps in species of Penicillium. Mycologia 27 (1935) 128-150
9. Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27 (1978) 401-410
10. Frisvad J.C., Filtenborg O., Lund F., and Samson R.A. The homogeneous species and series in subgenus Penicillium are related to mammal nutrition and excretion. In: Samson R.A., and Pitt J.I. (Eds). Integration of Modern Taxonomic Methods for Penicillium and Aspergillus Classification (2000), Harwood Academic Publishers, Amsterdam 265-283
11. Frisvad J.C., Filtenborg O., Samson R.A., and Stolk A.C. Chemotaxonomy of the genus Talaromyces. Anton. Leeuw. 57 (1990) 179-189
12. Frisvad J.C., and Samson R.A. Polyphasic taxonomy of Penicillium subgenus Penicillium A guide to identification of food and air-borne terverticillate penicillia and their mycotoxins. Stud. Mycol. 49 (2004) 1-173
13. Geiser D.M., Harbinski F.M., and Taylor J.W. Molecular and analytical tools for characterizing Aspergillus and Penicillium species at the intra-and interspecific levels. In: Samson R.A., and Pitt J.I. (Eds). Integration of Modern Taxonomic Methods for Penicillium and Aspergillus Classification (2000), Harwood Academic Publishers, Amsterdam 381-394
14. Glass N.L., and Donaldson G.C. Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous Ascomycetes. Appl. Environ. Microbiol. 61 (1995) 1323-1330
15. Grantham R., Gautier C., Gouy M., Mercier R., and Pavé A. Codon usage catalog and the gemome hypothesis. Nucl. Acids Res. 8 (1980) r49-r62
16. Hall T.A. Bioedit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. Ser. 41 (1999) 95-98
17. Hou Z.-C., and Yang N. Factors affecting codon usage in Yesinia pestis. Acta Biochem. Biophys. Sin. 35 (2003) 580-586
18. Lemke P.A. Speciation phemomena. In: McLaughlin D.J., McLaughlin E.G., and Lemke P.A. (Eds). The Mycota VII. Systemtics and Evolution Part B (2001), Springer-Verlag, Berlin Heidelberg 219-227
19. Liu Y.J., Whelen S., and Hall B.D. Phylogenetic relationships among Ascomycetes: evidence from an RNA polymerase II subunit. Mol. Biol. Evol. 16 (1999) 1799-1808
20. LoBuglio K.F., and Taylor J.W. Molecular phylogeny of Talaromyces and Penicillium species in Subgenus Biverticillium. In: Reynolds D.R., and Taylor J.W. (Eds). The Fungal Holomorph: Mitotic, Meiotic and Pleomorphic Speciation in Fungal Systematics (1993), CAB International, Wallingford 115-119
21. LoBuglio K.F., and Taylor J.W. Phylogeny and PCR detection of the human pathogenic fungus Penicillium marneffei. J. Clin. Microbiol. 33 (1995) 85-89
22. LoBuglio K.F., Pitt J.I., and Taylor J.W. Phylogenetic analysis of two ribosomal DNA regions indicates multiple independent losses of a sexual Talaromyces state among asexual Penicillium species in Subgenus Biverticillium. Mycologia 85 (1993) 592-604
23. LoBuglio K.F., Pitt J.I., and Taylor J.W. Independent origins of the synnematous Penicillium species, P. duclauxii, P. clavigerum, and P. vulpinum, assessed by two ribosomal DNA regions. Mycol. Res. 98 (1994) 250-256
24. Logrieco A., Peterson S.W., and Wicklow D.T. Ribosomal RNA comparisons among taxa of the terverticillate penicillia. In: Samson R.A., and Pitt J.I. (Eds). Modern Concepts in Penicillium and Aspergillus Classification (1990), Plenum Press, New York 343-355
25. Lynn D.J., Singer G.A.C., and Hickey A. Synonymous codon usage is subject to selection in thermophilic bacteria. Nucl. Acids Res. 30 (2002) 4272-4277
26. Ma J.-M., Zhou T., Gu W.-J., Sun X., and Lu Z.-H. Cluster analysis of the codon usage frequency of MHC genes from different species. BioSystems 65 (2002) 199-207
27. Malloch D. The Trichocomaceae: relationships with other ascomycetes. In: Samson R.A., and Pitt J.I. (Eds). Advances in Penicillium and Aspergillus Systematics (1985), Plenum Press, New York 365-382
28. Ogawa H., and Sugiyama J. Evolutonary relationships of the cleistothecial genera with Penicillium, Geosmithia, Merimbla and Sarophorum anamorphs as inferred from 18S rDNA sequence divergence. In: Samson R.A., and Pitt J.I. (Eds). Integration of Modern Taxonomic Methods for Penicillium and Aspergillus Classification (2000), Harwood Academic Publishers, Amsterdam 149-161
29. Ogawa H., Yoshimura A., and Sugiyama J. Polyphyletic origins of the anamorphic genus Geosmithia and the relationships of the cleistothecial genera: evidence from 18S 5S and 28S rDNA sequence analyses. Mycologia 89 (1997) 756-771
30. Peden, J.F., 1999. Analysis of codon usage. Thesis submitted to University of Nottingham for the degree of Doctor of Philosophy, August 1999, pp. 1-215.
31. Peterson S.W. Molecular genetic assessment of relatedness of Penicillium subgenus Penicillium. In: Reynolds D.R., and Taylor J.W. (Eds). The Fungal Holomorph: Mitotic, Meiotic and Pleomorphic Speciation in Fungal Systematics (1993), CAB International, Wallingford 121-128
32. Peterson S.W. Phylogenetic analysis of Penicillium species based on ITS and lsu-rDNA nucleotide sequences. In: Samson R.A., and Pitt J.I. (Eds). Integration of Modern Taxonomic Methods for Penicillium and Aspergillus Classification (2000), Harwood Academic Publishers, Amsterdam 163-178
33. Peterson S.W. Multilocus DNA sequence analysis shows that Penicillium biourgeanum is a distinct species closely related to P. brevicompactum and P. olsonii. Mycol. Res. 108 (2004) 434-440
34. Peterson S.W., Pérez J., Vega F.E., and Infante F. Penicillium brocae, a new species associated with the coffee borer in Chiapas. Mexico. Mycologia 95 (2003) 141-147
35. Peterson S.W., and Sigler L. Four new Penicillium species having Thysanophora-like melanized conidiophores. Mycol. Res. 106 (2002) 1109-1118
36. Pitt J.I. The Genus Penicillium and Its Teleomorphic States Eupenicillium and Talaromyces (1979), Academic Press, London
37. Pitt J.I. Phylogeny in the genus Penicillium: a morphologist's perspective. Can. J. Bot. 73 Suppl. 1 (1995) S768-S777
38. Pitt J.I., Samson R.A., and Frisvad J.C. List of accepted species and their synonyms in the family Trichocomaceae. In: Samson R.A., and Pitt J.I. (Eds). Integration of Modern Taxonomic Methods for Penicillium and Aspergillus Classification (2000), Harwood Academic Publishers, Amsterdam 9-49
39. Pitt J.I., and Samson R.A. Types of Aspergillus and Penicillium and their teleomorphs in current use. In: Samson R.A., and Pitt J.I. (Eds). Integration of Modern Taxonomic Methods for Penicillium and Aspergillus Classification (2000), Harwood Academic Publishers, Amsterdam 51-72
40. Raper K.B., Thom C., and Fennell D.I. A Manual of the Penicillia (1949), The Williams & Wilkins Company, Baltimore
41. 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
42. Samson, R.A., Hoekstra, E.H., Frisvad, J.C., Filtenborg, O., 2000. Introduction to Food and Airborne Fungi. 6th ed., second print. Centraalbureau voor Schimmelcultures, Utrecht.
43. Samson R.A., Seifert K.A., Kuijpers A.F.A., Houbraken J.A.M.P., and Frisvad J.C. Phylogenetic analysis of Penicillium subgenus Penicillium using partial-tubulin sequences. Stud. Mycol. 49 (2004) 175-200
44. Samson R.A., Stolk A.C., and Hadlok R. Revision of the subsection Fasciculata of Penicillium and some allied species. Stud. Mycol. 11 (1976) 1-45
45. Scott D.B. The genus Eupenicillium Ludwig. Res. Rep. Coun. Scient. Ind. Res. Pretoria 272 (1968) 1-150
46. Scott D.B., and Stolk A.C. Studies on the genus Eupenicillium Ludwig II. Perfect states of some penicillia. Anton. Leeuw. 33 (1967) 297-314
47. Scott J., Malloch D., Wong B., Sawa T., and Straus N. DNA heteroduplex fingerprinting in Penicillium. In: Samson R.A., and Pitt J.I. (Eds). Integration of Modern Taxonomic Methods for Penicillium and Aspergillus classification (2000), Harwood Academic Publishers, Amsterdam 225-236
48. Seifert K.A., and Louis-Seize G. Phylogeny and species concepts in the Penicillium aurantiogriseum complex as inferred from partial β-tubulin gene DNA sequences. In: Samson R.A., and Pitt J.I. (Eds). Integration of Modern Taxonomic Methods for Penicillium and Aspergillus Classification (2000), Harwood Academic Publishers, Amsterdam 189-198
49. Sharp P.M., Tuohy T.M.F., and Mosurski K.R. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucl. Acids Res. 14 (1986) 5125-5143
50. Sharp P.M., and Cowe E. Synonymous codon usage in Saccharomyces cerevisiae. Yeast 7 (1991) 657-678
51. Skouboe P., Boysen M., Pedersen L.H., Frisvad J.C., and Rossen L. Identification of Penicillium species using the internal transcribed spacer (ITS) regions. In: Rossen L., Rubio V., Dawson M.T., and Frisvad J.C. (Eds). Fungal Identification Techniques (1996), European Commission, Brussels, Belgium 160-164
52. Skouboe P., Frisvad J.C., Taylor J.W., Lauritsen D., Boysen M., and Rossen L. Phylogenetic analysis of nucleotide sequences from the ITS region of terverticillate Penicillium species. Mycol. Res. 103 (1999) 873-881
53. Skouboe P., Taylor J.W., Frisvad J.C., Lauritsen D., Larsen L., Alboek C., Boysen M., and Rossen L. Molecular methods for differentiation of closely related Penicillium species. In: Samson R.A., and Pitt J.I. (Eds). Integration of Modern Taxonomic Methods for Penicillium and Aspergillus classification (2000), Harwood Academic Publishers, Amsterdam 179-188
54. Stolk A.C. Studies on the genus Eupenicillium Ludwig III. Four new species of Eupenicillium. Anton. Leeuw. 34 (1968) 37-53
55. Stolk A.C., and Samson R.A. Hamigera gen. nov. and Byssochlamys Studies on Talaromyces and related genera I. Persoonia 6 (1971) 341-357
56. Stolk A.C., and Samson R.A. The genus Talaromyces. Studies on Talaromyces and related Ggnera II. Stud. Mycol. 2 (1972) 1-65
57. Stolk A.C., and Samson R.A. The ascomycete genus Eupenicillium and related Penicillium anamorphs. Stud. Mycol. 23 (1983) 1-149
58. Stolk A.C., and Scott D.B. Studies on the Genus Eupenicillium Ludwig I. Taxonomy and nomenclature of Penicillium in relation to their sclerotial ascocarpic states. Persoonia 4 (1967) 391-405
59. *and other methods). Version 4 (2001), Sinauer Associates, Sunderland, MA
60. Thompson J.D., Gibbson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res. 25 (1997) 4876-4882
61. Tuthill D.E., Frisvad J.C., and Christensen M. Systematics of Penicillium simplicissimum based on rDNA sequences, morphology and secondary metabolites. Mycologia 93 (2001) 298-308
62. Wang L., Zhou H.-B., Frisvad J.C., and Samson R.A. Penicillium persicinum, a new griseolfulvin, chrysogine and roquefortine C producing species from Qinghai province, China. Anton. Leeuw. 86 (2004) 173-179
63. Wang L., and Zhuang W.-Y. Designing primer sets for amplification of partial calmodulin genes from penicillia. Mycosystema 23 (2004) 466-473
64. Williams A.P., Pitt J.I., and Hocking A.D. The closely related species of subgenus Penicillium - a phylogenic exploration. In: Samson R.A., and Pitt J.I. (Eds). Integration of Modern Taxonomic Methods for Penicillium and Aspergillus classification (1985), Harwood Academic Publishers, Amsterdam 121-128
65. Zhang N., and Blackwell M. Molecular phylogeny of Melanospora and similar pyrenomycetous fungi. Mycol. Res. 106 (2000) 148-155