Identifying and Naming Plant-Pathogenic Fungi: Past, Present, and Future

Annual Review of Phytopathology

Volumn 53, Issue , 2015, Pages 247-267

  Crous, Pedro W ^a,b,f   Hawksworth, David L ^c,d,e   Wingfield, Michael J ^f  

^a CBS KNAW FUNGAL BIODIVERSITY CENTRE   (Netherlands)

^b WAGENINGEN UNIVERSITY   (Netherlands)

^c UNIVERSIDAD COMPLUTENSE DE MADRID   (Spain)

^d DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

^e ROYAL BOTANIC GARDENS   (United Kingdom)

^f UNIVERSITY OF PRETORIA   (South Africa)

Author keywords

Code of Nomenclature; DNA barcoding; MycoBank; Phylogeny; Polyphasic identification; Systematics

Indexed keywords

FUNGI;

BIODIVERSITY; CLASSIFICATION; CROP; FUNGUS; GENOMICS; MICROBIOLOGY; PHYSIOLOGY; PLANT DISEASE;

BIODIVERSITY; CROPS, AGRICULTURAL; FUNGI; GENOMICS; PLANT DISEASES; PLANT PATHOLOGY;

EID: 84938696821     PISSN: 00664286     EISSN: 15452107     Source Type: Book Series    
DOI: 10.1146/annurev-phyto-080614-120245     Document Type: Article

References (115)

1. Amend AS, Seifert KA, Samson R, Bruns TD. 2010. Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics. Proc. Natl. Acad. Sci. USA 107:13748-53
2. Andersen B, Sorensen JL, Nielsen KF, Gerrits van den Ende B, de Hoog GS. 2009.Apolyphasic approach to the taxonomy of the Alternaria infectoria species-group. Fungal Genet. Biol. 46:642-56
3. Ariyawansa HA, Hawksworth DL, Hyde KD, Gareth Jones EB, Maharachchikumbura SSN, et al. 2014. Epitypification and neotypification: guidelines with appropriate and inappropriate examples. Fungal Divers. 69:57-91
4. Bearchell SJ, Fraaije BA, Shaw MW, Fitt BDL. 2005. Wheat archive links long-term fungal pathogen population dynamics to air pollution. Proc. Natl. Acad. Sci. USA 102:5438-42
5. Berbee ML, Taylor JW. 1992. 18S ribosomal RNA gene sequence characters place the human pathogen Sporothrix schenckii in the genus Ophiostoma. Exp. Mycol. 16:87-91
6. Berkeley MJ. 1846. Observations, botanical and physiological, on the potato murrain. J. R. Hortic. Soc. 1:9-34
7. Bidartondo MI, Bruns TD, Blackwell M, Edwards I, Taylor AFS, et al. 2008. Preserving accuracy in GenBank. Science 319:1616
8. Blackwell M. 2011. The fungi: 1, 2, 3. . 5.1 million species? Am. J. Bot. 98:426-38
9. Blackwell M, Hibbett DS, Taylor JW, Spatafora JW. 2006. Research coordination networks: A phylogeny for kingdom Fungi (Deep Hypha). Mycologia 98:829-37
10. Brasier CM, Kirk SA. 2001. Designation of the EAN and NAN races of Ophiostoma novo-ulmi as subspecies. Mycol. Res. 105:547-54
11. Bruns TD, White TJ, Taylor JW. 1991. Fungal molecular systematics. Annu. Rev. Ecol. Syst. 22:525-64
12. Buée M, Reich M, Murat C, Morin E, Nilsson RH, et al. 2009. 454 pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol. 184:449-56
13. Cai L, Hyde KD, Taylor PWJ, Weir BS, Waller JM, et al. 2009. A polyphasic approach for studying Colletotrichum. Fungal Divers. 39:183-204
14. Cannon PF, Damm U, Johnston PR, Weir BS. 2012. Colletotrichum: current status and future directions. Stud. Mycol. 73:181-213
15. Carmichael JW, Sekhon AS, Sigler L. 1973. Classification of some dermatophytes by pyrolysis-gas-liquid chromatography. Can. J. Microbiol. 19:403-7
16. Cheewangkoon R, Groenewald JZ, Hyde KD, To-anun C, Crous PW. 2012. Chocolate spot of Eucalyptus. Mycol. Prog. 11:61-69
17. Chupp C. 1954. A Monograph of the Fungus Genus Cercospora. Ithaca, NY
18. Cole GT, Samson RA. 1979. Patterns of Development in Conidial Fungi. London: Pitman Publ
19. Crous PW. 1998. Mycosphaerella spp. And Their Anamorphs Associated with Leaf Spot Diseases of Eucalyptus. St. Paul, MN: APS Press
20. Crous PW, Braun U, Hunter GC, Wingfield MJ, Verkley GJM, et al. 2013. Phylogenetic lineages in Pseudocercospora. Stud. Mycol. 75:37-114
21. Crous PW, Gams W, Stalpers JA, Robert V, Stegehuis G. 2004. MycoBank: An online initiative to launch mycology into the 21st century. Stud. Mycol. 50:19-22
22. Crous PW, Giraldo A, Hawksworth DL, Robert V, Kirk PM, et al. 2014. The Genera of Fungi: fixing the application of type species of generic names. IMA Fungus 5:141-60
23. Crous PW, Slippers B, Wingfield MJ, Rheeder J, Marasas WFO, et al. 2006. Phylogenetic lineages in the Botryosphaeriaceae. Stud. Mycol. 55:235-53
24. Damm U, Cannon PF, Woudenberg JHC, Crous PW. 2012. The Colletotrichum acutatum species complex. Stud. Mycol. 73:37-113
25. Damm U, Cannon PF, Woudenberg JHC, Johnston PR, Weir BS, et al. 2012. The Colletotrichum boninense species complex. Stud. Mycol. 73:1-36
26. de Beer ZW, Duong TA, Barnes I, Wingfield BD, Wingfield MJ. 2014. Redefining Ceratocystis. Stud. Mycol. 79:187-219
27. de Queiroz K. 2007. Species concepts and species delimitation. Syst. Biol. 56:879-86
28. Dickie IA, FitzJohn RG. 2007. Using terminal restriction fragment length polymorphism (T-RFLP) to identify mycorrhizal fungi: A methods review. Mycorrhiza 17:259-70
29. Federhen S. 2015. Type material in the NCBI Taxonomy Database. Nucleic Acids Res. 43:D1086-98
30. Fuckel L. 1870. Symbolae mycologicae. Beiträge zur Kenntniss der Rheinischen Pilze. Jahrb. des Nassauischen Vereins f ür Naturk 23-24:1-459
31. Gams W, Humber RA, JaklitschW, Kirschner R, Stadler M. 2012. Minimizing the chaos following the loss of Article 59: suggestions for a discussion. Mycotaxon 119:495-507
32. Gargouri S, Hamza S, Hajlaoui MR. 2006. AFLP analysis of the genetic variability and population structure of the wheat crown rot fungus Fusarium pseudograminearum in Tunisia. Tunis. J. Plant Prot. 1:93-104
33. Gibbons A. 2013. On the trail of ancient killers. Science 340:1278-82
34. GreuterW, Garrity G, Hawksworth DL, Jahn R, Kirk PM, et al. 2011. Draft BioCode 2011: principles and rules regulating the naming of organisms. Taxon 60:201-12
35. Groenewald JZ, Nakashima C, Nishikawa J, Shin H-D, Park J-H, et al. 2013. Species concepts in Cercospora: spotting the weeds among the roses. Stud. Mycol. 75:115-70
36. Groenewald M, Barnes I, Bradshaw RE, Brown AV, Dale A, et al. 2007. Characterization and distribution of mating type genes in the Dothistroma needle blight pathogens. Phytopathology 97:825-34
37. Groenewald M, Groenewald JZ, Braun U, Crous PW. 2006. Host range of Cercospora apii and C. beticola, and description of C. Apiicola, a novel species from celery. Mycologia 98:275-85
38. Hansen K, Lobuglio KF, Pfister DH. 2005. Evolutionary relationships of the cup-fungus genus Peziza and Pezizaceae inferred from multiple nuclear genes: RPB2, beta-tubulin, and LSU rDNA. Mol. Phyl. Evol. 36:1-23
39. Harrington TC, Rizzo DM. 1999. Defining species in the fungi. In Structure and Dynamics of Fungal Populations, ed. JJ Worrall, pp. 43-70. Dordrecht, Neth.: Kluwer Acad
40. Hall R. 1969. Molecular approaches to taxonomy of fungi. Bot. Rev. 35:285-304
41. Hawksworth DL. 1991. The fungal dimension of biodiversity: magnitude, significance, and conservation. Mycol. Res. 95:641-55
42. Hawksworth DL. 1996. Microbial collections as a tool in biodiversity and biosystematic research. In Culture Collections to Improve the Quality of Life, ed. RA Samson, JA Stalpers, D van derMei, AHStouthamer, pp. 26-35. Baarn, Neth.: Centraalbureau voor Schimmelcultures
43. Hawksworth DL. 2004. (183-187) Limitation of dual nomenclature for pleomorphic fungi. Taxon 53:596-98
44. Hawksworth DL. 2012. Global species numbers of fungi: Are tropical studies and molecular approaches contributing to a more robust estimate? Biodivers. Conserv. 21:2425-33
45. Hawksworth DL, Crous PW, Redhead SA, Reynolds DR, Samson RA, et al. 2011. The Amsterdam Declaration on Fungal Nomenclature. IMA Fungus 2:105-12
46. Hibbett DS, Ohman A, Glotzer D, Nuhn M, Kirk PM, et al. 2011. Progress in molecular and morphological taxon discovery and options for formal classification of environmental sequences. Fungal Biol. Rev. 25:38-47
47. Hyde KD, Jones EBG, Lui J-K, Ariyawansa H, Boehm E, et al. 2013. Families of Dothideomycetes. Fungal Divers. 63:1-313
48. Johnston PR, Seifert KA, Stone JK, Rossman AY, Marvanová L. 2014. Recommendations on generic names competing for use in Leotiomycetes (Ascomycota). IMA Fungus 5:91-120
49. Kemler M, Garnas J, Wingfield MJ, Gryzenhout M, Pillay K-A, et al. 2013. Ion Torrent PGM as tool for fungal community analysis: A case study of endophytes in Eucalyptus grandis reveals high taxonomic diversity. PLOS ONE 8:e81718
50. Kendrick B, ed. 1979. The Whole Fungus: The Sexual-Asexual Synthesis, Vols. 1, 2. Ottawa: Natl. Mus. Can
51. Kirk PM, Stalpers JA, Braun U, Crous PW, Hansen K, et al. 2013. A without-prejudice list of generic names of fungi for protection under the International Code of Nomenclature for algae, fungi and plants. IMA Fungus 4:381-443
52. Klaubauf S, Tharreau D, Fournier E, Groenewald JZ, Crous PW, et al. 2014. Resolving the polyphyletic nature of Pyricularia (Pyriculariaceae). Stud. Mycol. 79:85-120
53. Kõljalg U, Henrik Nilsson R, Abarenkov K, Tedersoo L, Taylor AFS, et al. 2013. Towards a unified paradigm for sequence-based identification of fungi. Mol. Ecol. 22:5271-77
54. Leslie JF. 1993. Fungal vegetative compatibility. Annu. Rev. Phytopathol. 31:127-50
55. Leslie JF, Summerell BA, eds. 2006. The Fusarium Laboratory Manual. Ames, IA: Blackwell Publ
56. Manamgoda DS, Rossman AY, Castlebury LA, Crous PW, Madrid H, et al. 2014. The genus Bipolaris. Stud. Mycol. 79:221-88
57. Martin MD, Cappellini E, Samaniego JA, Zepeda ML, Campos PF, et al. 2013. Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. Nat. Commun. 4:2172
58. Mayden RL. 1997. A hierarchy of species concepts: the denouncement in the saga of the species problem. In Species: The Units of Diversity, ed. MF Claridge, HA Dawah, MR Wilson, pp. 381-424. London: Chapman & Hall
59. McNeill J, Barrie FR, Buck WR, Demoulin V, GreuterW, et al., eds. 2012. International Code of Nomenclature for Algae, Fungi, and Plants (Melbourne Code). Regnum Vegetabile Königstein, Germ.: Koeltz Sci. Books
60. Micales JA, BondeMR, Peterson GL. 1986. The use of isozyme analysis in fungal taxonomy and genetics. Mycotaxon 27:405-49
61. Mostert L, Crous PW, Kang C-J, Phillips AJL. 2001. Species of Phomopsis and a Libertella sp. Occurring on grapevines with specific reference to South Africa: morphological, cultural, molecular and pathological characterization. Mycologia 93:145-66
62. Mostert L, Groenewald JZ, Summerbell RC, Gams W, Crous PW. 2006. Taxonomy and pathology of Togninia (Diaporthales) and its Phaeoacremonium anamorphs. Stud. Mycol. 54:1-115
63. Ni M, Feretzaki M, Sun S, Wang X, Heitman J. 2011. Sex in fungi. Annu. Rev. Genet. 45:405-30
64. Nilsson RH, Hyde KD, Pawlowska J, Ryberg M, Tedersoo L, et al. 2014. Improving ITS sequence data for identification of plant pathogenic fungi. Fungal Divers. 67:11-19
65. Nilsson RH, Ryberg M, Kristiansson E, Abarenkov K, Larsson K-H, et al. 2006. Taxonomic reliability of DNA sequences in public sequence databases: A fungal perspective. PLOS ONE 1:e59
66. OBrien BL, Parrent JL, Jackson JA, Moncalvo JM, Vilgalys R. 2005. Fungal community analysis by large-scale sequencing of enviromental samples. Appl. Environ. Microbiol. 71:5544-50
67. ODonnell K, Cigelnik E, Nirenberg HI. 1998. Molecular systematics and phylogeography of the Gibberella fujikuroi species complex. Mycologia 90:465-93
68. ODonnell K, KistlerHC, TackeBK, CasperHH.2000. Gene genealogies reveal global phylogeographic structure and reproductive isolation among lineages of Fusarium graminearum, the fungus causing wheat scab. Proc. Natl. Acad. Sci. USA 97:7905-10
69. Ohm RA, Feau N, Henrissat B, Schoch CL, Horwitz BA, et al. 2012. Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLOS Pathog. 8:e1003037
70. Opik M, Metsis M, Daniell TJ, Zobel M, Moora M. 2009. Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest. New Phytol. 184:424-37
71. Ovaskainen O, Nokso-Koivisto J, Hottola J, Rajala T, Pennanen T, et al. 2010. Identifying woodinhabiting fungi with 454 sequencing: What is the probability that BLAST gives the correct species? Fungal Ecol. 3:274-83
72. Petrini LE. 1992. Rosellinia species of the temperate zones. Sydowia 44:169-281
73. Phillips AJL, Alves A, Abdollahzadeh J, Slippers B, Wingfield MJ, et al. 2013. The Botryosphaeriaceae: genera and species known from culture. Stud. Mycol. 76:51-167
74. Quaedvlieg W, Binder M, Groenewald JZ, Summerell BA, Carnegie AJ, et al. 2014. Introducing the consolidated species concept to resolve species in the Teratosphaeriaceae. Persoonia 33:1-40
75. Quaedvlieg W, Kema GHJ, Groenewald JZ, Verkley GJM, Seifbarghi S, et al. 2011. Zymoseptoria gen. Nov.: A new genus to accommodate Septoria-like species occurring on graminicolous hosts. Persoonia 26:57-69
76. Redhead SA, Demoulin V, Hawksworth DL, Seifert KA, Turland NJ. 2014. Fungal nomenclature at IMC10: report of the nomenclature sessions. IMA Fungus 5:449-62
77. Reynolds DR, Taylor JW. 1991. DNA specimens and the "International Code of Botanical Nomenclature." Taxon 40:311-15
78. Richards RA. 2010. The Species Problem: A Philosophical Analysis. Cambridge, UK: Cambridge Univ. Press
79. Robert V, Vu D, Amor ABH, van de Wiele N, Brouwer C, et al. 2013. MycoBank gearing up for new horizons. IMA Fungus 4:371-79
80. Ropars J, López-Villavicencio M, Dupont J, Snirc A, Gillot G, et al. 2014. Induction of sexual reproduction and genetic diversity in the cheese fungus Penicillium roqueforti. Evol. Appl. 7:433-41
81. Rossman AY, Seifert KA, Samuels GJ, Minnis AW, Schroers HJ, et al. 2013. Genera in Bionectriaceae, Hypocreaceae, and Nectriaceae (Hypocreales) proposed for acceptance or rejection. IMA Fungus 4:41-51
82. Roux J, Greyling I, Coutinho TA, Verleur M, Wingfield MJ. 2013. The Myrtle rust pathogen, Puccinia psidii, discovered in Africa. IMA Fungus 4:155-59
83. Saccardo PA. 1882-86. Sylloge Fungorum, Vols. 1-4. Padova: P.A. Saccardo
84. Samson RA, Noonim P, Meijer M, Houbraken J, Frisvad JV, et al. 2007. Diagnostic tools to identify black aspergilli. Stud. Mycol. 59:129-46
85. Schoch CL, Crous PW, Wingfield MJ, Wingfield BD. 2000. Phylogeny of Calonectria and selected hypocrealean genera with cylindrical macroconidia. Stud. Mycol. 45:45-62
86. Schoch CL, Robbertse B, Robert V, Vu D, Cardinali G, et al. 2014. Finding needles in for fungi. Haystacks: linking scientific names, reference specimens and molecular data for Fungi. Database. doi:10.1093/database/bau061
87. Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, et al. 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc. Natl. Acad. Sci. USA 109:6241-46
88. Scott PM, Lawrence JW, vanWalbeek W. 1970. Detection ofmycotoxins by thin-layer chromatography: Application to screening of fungal extracts. Appl. Microbiol. 20:839-42
89. Seifert KA, ed. 2003. Has dual nomenclature for fungi run its course? The Article 59 debate. Mycotaxon 88:493-508
90. Seifert KA, Rossman AY. 2010. How to describe a new fungal species. IMA Fungus 1:109-16
91. Shivas RG, Beasley DR, McTaggart AR. 2014. Online identification guides for Australian smut fungi (Ustilaginomycotina) and rust fungi (Pucciniales). IMA Fungus 5:195-202
92. Silva-Mann R, Vieira MGGC, Machado JC, Bernardino Filho JR, Salgado KCC, et al. 2005. AFLP markers differentiate Colletotrichum gossypii from C. gossypii var. Cephalosporioides. Fitopatol. Bras. 30:169-72
93. Slippers B, Boissin E, Phillips AJL, Groenewald JZ, Wingfield MJ, et al. 2013. Phylogenetic lineages in the Botryosphaeriales: A systematic and evolutionary framework. Stud. Mycol. 76:31-49
94. Stadler M, Læssoe T, Fournier J, Decock C, Schmieschek B, et al. 2014. A polyphasic taxonomy of Daldinia (Xylariaceae). Stud. Mycol. 77:1-143
95. Storck R, Alexopoulos CJ, Phaff HJ. 1969. Nucleotide composition of deoxyribonucleic acid of some species of Cryptococcus, Rhodotorula, and Sporobolomyces. J. Bacteriol. 98:1069-72
96. Su YY, Cai L. 2012. Polyphasic characterisation of three new Phyllosticta spp. Persoonia 28:76-84
97. Takamatsu S, Kano Y. 2001. PCR primers useful for nucleotide sequencing of rDNA of the powdery mildew fungi. Mycoscience 42:135-39
98. Taylor DL, Hollingsworth TN, McFarland JW, et al. 2013. A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning. Ecol. Monogr. 84:3-20
99. Taylor JW, Jacobson DJ, Kroken S, Kasuga T, Geiser DM, et al. 2000. Phylogenetic species recognition and species concepts in fungi. Fungal Genet. Biol. 31:21-32
100. Taylor TN, Krings M, Taylor EJ. 2014. Fossil Fungi. London: Elsevier Acad. 1st ed
101. Tehler A. 1993. Schismatomma and three new or reinstated genera, a reassessment of generic relationships in Arthoniales. Cryptogam. Bot. 3:139-51
102. Tulasne LR, Tulasne C. 1865. Selecta Fungorum Carpologia: Nectriei-Phacidiei-Pezizei, Vol. 1. Paris: Imp. Typogr. Parisiis
103. van der Nest MA, Bihon W, De Vos L, Naidoo K, Roodt D, et al. 2014. Draft genome sequences of Diplodia sapinea, Ceratocystis manginecans, and Ceratocystis moniliformis. IMA Fungus 5:135-40
104. van Driel KGA, Humbel BM, Verkleij AJ, Stalpers J, Müller WH, Boekhout T. 2009. Septal pore complex morphology in the Agaricomycotina (Basidiomycota) with emphasis on the Cantharellales and Hymenochaetales. Mycol. Res. 113:559-76
105. Varga J, Frisvad JC, Samson RA. 2010. Polyphasic taxonomy of Aspergillus section Sparsi. IMA Fungus 1:187-95
106. von Arx JA, van der Walt JP, Liebenberg NVDM. 1982. The classification of Taphrina and other fungi with yeast-like cultural states. Mycologia 74:285-96
107. Wang H-K, Aptroot A, Crous PW, Hyde KD, Jeewon R. 2007. The polyphyletic nature of Pleosporales: An example from Massariosphaeria based on rDNA and RPB2 gene phylogenies. Mycol. Res. 111:1268-76
108. Weresub LK, Pirozynski KA. 1979. Pleomorphism of fungi as treated in the history of mycology and nomenclature. In The Whole Fungus, Vol. 1, ed. B Kendrick, pp. 17-25. Ottawa: Natl. Mus. Can
109. White TJ, Bruns T, Lee S, Taylor W. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR Protocols: A Guide to Methods and Applications, ed. M Innis, D Gelfand, J Sninsky, T White, pp. 315-22. San Diego, CA: Academic Press
110. WielochW. 2006. Chromosome visualisation in filamentous fungi. J. Microbiol. Meth. 67:1-8
111. Wijayawardene NN, Crous PW, Kirk PM, Hawksworth DL, Boonmee S, et al. 2014. Naming and outline of Dothideomycetes-2014 including proposals for the protection or suppression of generic names. Fungal Divers. 69:1-55
112. Wikee S, Lombard L, Nakashima C, Motohashi K, Chukeatirote E, et al. 2013. A phylogenetic reevaluation of Phyllosticta (Botryosphaeriales). Stud. Mycol. 76:1-29
113. Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV. 1990. DNA polymorphisms amplified by
114. Wingfield MJ, De Beer ZW, Slippers B, Wingfield BD, Groenewald JZ, et al. 2012. One fungus, one name promotes progressive plant pathology. Mol. Plant Pathol. 13:604-13
115. Woudenberg JHC, Truter M, Groenewald JZ, Crous PW. 2014. Large-spored Alternaria pathogens in section Porri disentangled. Stud. Mycol. 79:1-47