A multi-locus phylogenetic evaluation of Diaporthe (Phomopsis)

Fungal Diversity

Volumn 56, Issue 1, 2012, Pages 157-171

  Udayanga, Dhanushka ^a,b   Liu, Xingzhong ^b   Crous, Pedro W ^c   McKenzie, Eric H C ^d   Chukeatirote, Ekachai ^a   Hyde, Kevin D ^a  

^a MAE FAH LUANG UNIVERSITY   (Thailand)

^b INSTITUTE OF MICROBIOLOGY   (China)

^c CBS KNAW FUNGAL BIODIVERSITY CENTRE   (Netherlands)

^d LANDCARE RESEARCH   (New Zealand)

Author keywords

Ex type culture; Host diversity; Mating types; Molecular systematics; New combination; Phytopathogen; Species recognition; Taxonomy

Indexed keywords

DIAPORTHE; FUNGI; PHOMOPSIS;

EID: 84866060109     PISSN: 15602745     EISSN: 18789129     Source Type: Journal    
DOI: 10.1007/s13225-012-0190-9     Document Type: Article

References (96)

1. Alves A, Correia A, Phillips AJL (2006) Multi-gene genealogies and morphological data support Diplodia cupressi sp. nov., previously recognized as D. pinea f. sp. cupressi, as a distinct species. Fungal Divers 23:1-15
2. Aoki T, O'Donell K, Scandiani MM (2005) Sudden death syndrome of soybean in South America is caused by four species of Fusarium: Fusarium brasiliense sp. nov., F. cuneirostrum sp. nov., F. tucumaniae, and F. virguliforme. Mycoscience 46:162
3. Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T, Neigel JE, Reeb CA, Saunders NC (1987) Intraspecific Phylogeography: the Mitochondrial DNA Bridge between Population Genetics and Systematics. Ann Rev Ecol Syst 18:489-522
4. Botella L, Diez JJ (2011) Phylogenic diversity of fungal endophytes in Spanish stands of Pinus halepensis. Fungal Divers 47:9-18
5. Cai L, Giraud T, Zhang N, Begerow D, Cai G, Shivas RG (2011a) The evolution of species concepts and species recognition criteria in plant pathogenic fungi. Fungal Divers 50:121-133
6. Cai L, Udayanga D, Manamgoda DS, Maharachchikumbura SSN, Liu XZ, Hyde KD (2011b) The need to carry out re-inventory of tropical plant pathogens. Trop Plant Pathol 36:205-213
7. Carbone I, Kohn L (1999) A method for designing primer sets for speciation studies in filamentous ascomycetes. Mycologia 91:553-556
8. Castlebury L (2005) The Diaporthe vaccinii complex of fruit pathogens. Inoculum 56:12
9. Castlebury LA, Farr DF, Rossman AY (2001) Phylogenetic distinction of Phomopsis isolates from cucurbits. Inoculum 52:25
10. Castlebury LA, Farr DF, Rossman AY, Jaklitsch WJ (2003) Diaporthe angelicae comb. nov., a modern description and placement of Diaporthopsis in Diaporthe. Mycoscience 44:203-208
11. Catalano V, Rekab D, Firrao G, Vannacci G, Vergara EM (2012) An endopolygalacturonase gene of Diaporthe helianthi. Phytopathol Mediterr 51:23-36
12. Choi YW, Hyde KD, Ho WH (1999) Single spore isolation of fungi. Fungal Divers 3:29-38
13. Chomnunti P, Schoch CL, Aguirre-Hudson B, Ko-Ko TW, Hongsanan S, Jones EBG, Kodsueb R, Phookamsak R, Chukeatirote E, Bahkali AH, Hyde KD (2011) Capnodiaceae. Fungal Divers 51:103-134
14. Coetzee MPA, Wingfield BD, Bloomer P, Wingfield MJ (2005) Phylogenetic analyses of DNA sequences reveal species partitions amongst isolates of Armillaria from Africa. Mycol Res 109:1223-1234
15. Cowley RB, Ash GJ, J Harper JDI, Luckett DJ (2012) Evaluation of resistance to Phomopsis stem blight (caused by Diaporthe toxica) in Lupinus albus. Eur J Plant Pathol. 133:631-644
16. Crouch JA, Clarke BB, Hillman BI (2009) What is the value of ITS sequence data in Colletotrichum systematics and species diagnosis? A case study using the falcate-spored graminicolous Colletotrichum group. Mycologia 101:648-656
17. Crous PW (2005) Impact of molecular phylogenetics on the taxonomy and diagnostics of fungi. Bull OEPP/EPPO 35:47-51
18. Crous PW, Groenewald JZ (2005) Hosts, species and genotypes: opinions versus data. Australas Plant Pathol 34:463-470
19. 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
20. Crous PW, Groenewald JZ, Groenewald M, Caldwell P, Braun U, Harrington TC (2006) Species of Cercospora associated with grey leaf spot of maize. Stud Mycol 55:189-197
21. Crous PW, Groenewald JZ, Shivas RG, Edwards J, Seifert KA et al (2011) Fungal planet description sheets: 69-91. Persoonia 26:108-156
22. Damm U, Cannon PF, Woudenberg JHC, Johnston PR, Weir BS, Tan YP, Shivas RG, Crous PW (2012) The Colletotrichum boninense species complex. Stud Mycol 73:1-36
23. r genes. J Plant Pathol 85:43-52
24. Diogo ELF, Santos JM, Phillips AJL (2010) Phylogeny, morphology and pathogenicity of Diaporthe and Phomopsis species on almond in Portugal. Fungal Divers 44:107-115
25. Einax E, Voigt K (2003) Oligonucleotide primers for the universal amplification of β-tubulin genes facilitate phylogenetic analyses. Organ Divers Evol 3:185-194
26. Farr DF, Castlebury LA, Rossman AY, Putnam ML (2002b) A new species of Phomopsis causing twig dieback of Vaccinium vitis-idaea (lingonberry). Mycol Res 106:745-752
27. Farr DF, Castlebury LA, Rossman AY (2002b) Morphological and molecular characterization of Phomopsis vaccinii and additional isolates of Phomopsis from blueberry and cranberry in the eastern United States. Mycologia 94:494-504
28. Farris JS, Kallersjo M, Kluge AG, Bult C (1994) Testing significance of incongruence. Cladistics 10:315-320
29. Garcia-Guzman G, Morales E (2007) Life-history strategies of plant pathogens: distribution patterns and phylogenetic analysis. Ecology 88:589-596
30. Garcia-Reyne A, López-Medrano F, Morales JM, García Esteban C, Martín I, Eraña I, Meije Y, Lalueza A, Alastruey-Izquierdo A, Rodríguez-Tudela JL, Aguado JM (2011) Cutaneous infection by Phomopsis longicolla in a renal transplant recipient from Guinea: first report of human infection by this fungus. Transpl Infect Dis 13:204-207
31. Glass NL, Donaldson GC (1995) Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes. Appl Environ Microbiol 61:1323-1330
32. Glienke C, Pereira OL, Stringari D, Fabris J, Kava-Cordeiro V, Galli-Terasawa L, Cunnington J, Shivas RG, Groenewald JZ, Crous PW (2011) Endophytic and pathogenic Phyllosticta species, with reference to those associated with Citrus Black Spot. Persoonia 26:47-56
33. Groenewald M, Groenewald JZ, Crous PW (2005) Distinct species exist within the Cercospora apii morphotype. Phytopathology 95:951-959
34. Hawksworth DL (2011) A new dawn for the naming of fungi: impacts of decisions made in Melbourne in July 2011 on the future publication and regulation of fungal names. IMA Fungus 2:155-162
35. Hofstetter V, Miadlikowska J, Kauff F, Lutzoni F (2007) Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: a case study of the Lecanoromycetes (Ascomycota). Mol Phylogenet Evol 44:412-426
36. Hudson RR, Coyne JA (2002) Mathematical consequences of the genealogical species concept. Evolution 56:1557-1565
37. Hyde KD, McKenzie EHC, KoKo TW (2011) Towards incorporating anamorphic fungi in a natural classification checklist and notes for 2010. Mycosphere 2:1-88
38. Iriart I, Binois R, Fior R, Blanchet R, Berry A, Cassaing S, Amazan E, Papot E, Carm B, Aznar C, Couppié P (2011) Eumycetoma caused by Diaporthe phaseolorum (Phomopsis phaseoli): a case report and a mini-review of Diaporthe/Phomopsis spp invasive infections in humans. Clin Microbiol Infec 17:1492-1494
39. James TY, Kauff F, Schoch CL, Matheny PB, Hofstetter V, Cox CJ, Celio G, Gueidan C, Fraker E, Miadlikowska J, Lumbsch HT, Rauhut A, Reeb V et al (2006) Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443:818-822
40. Jiang SX, Ma HB (2010) A new species of Phomopsis on Castanea mollisima. Mycosystema 29:467-471
41. Jurković D, Vrandečić K, C̈osić J, Riccioni L, Duvnjak T (2007) Morphological identification of Diaporthe/Phomopsis sp. isolated from Xanthium italicum. Poljoprivreda (Osijek) 13:10-14
42. Kanematsu S, Adachi Y, Ito T (2007) Mating-type loci of heterothallic Diaporthe spp. homologous genes are present in opposite mating-types. Curr Genet 52:11-22
43. Katoh K, Toh H (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9:276-285
44. Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059-3066
45. Kishino H, Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J Mol Evol 29:170-179
46. Lombard L, Crous PW, Wingfield BD, Wingfield MJ (2010) Phylogeny and systematics of the genus Calonectria. Stud Mycol 66:31-69
47. Lumbsch HT, Schmitt I, Lindemuth R, Miller A, Mangold A, Fernandez F, Huhndorf S (2005) Performance of four ribosomal DNA regions to infer higher-level phylogenetic relationships of inoperculate euascomycetes (Leotiomyceta). Mol Phylogenet Evol 34:512-524
48. Manamgoda DS, Cai L, Bahkali AH, Chukeatirote E, Hyde KD (2011) Cochliobolus: an overview and current status of species. Fungal Divers 51:3-42
49. McNeill J, Turland NJ, Monro A, Lepschi BJ (2011) XVIII International Botanical Congress: preliminary mail vote and report of Congress action on nomenclature proposals. Taxon 60:1507-1520
50. Mejía LC, Castlebury LA, Rossman AY, Sogonov MV, White JF Jr (2011) A systematic account of the genus Plagiostoma (Gnomoniaceae, Diaporthales) based on morphology, host-associations, and a four-gene phylogeny. Stud Mycol 68:211-235
51. Mejia LC, Rossman AY, Castlebury LA, White JF Jr (2011) New species, phylogeny, host-associations, and geographic distribution of the genus Cryptosporella (Gnomoniaceae, Diaporthales). Mycologia 103:379-399
52. Moleleki N, Preisig O, Wingfield MJ, Crous PW, Wingfield BD (2002) PCR-RFLP and sequence data delineate three Diaporthe species associated with stone and pome fruit trees in South Africa. Eur J Plant Pathol 108:909-912
53. Mostert L, Crous PW, Kang JC, 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 93:146-167
54. Murali TS, Suryanarayanan TS, Geeta R (2006) Endophytic Phomopsis species: host range and implications for diversity estimates. Can J Microbiol 52:673-680
55. Page RDM (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357-358
56. Phillips AJL, Crous PW, Alves A (2007) Diplodia seriata, the anamorph of Botryosphaeria obtusa. Fungal Divers 25:141-155
57. Phoulivong S, Cai L, Chen H, McKenzie EHC, Abdelsalam K, Chukeatirote E, Hyde KD (2010) Colletotrichum gloeosporioides is not a common pathogen on tropical fruits. Fungal Divers 44:33-43
58. Rehner SA, Uecker FA (1994) Nuclear ribosomal internal transcribed spacer phylogeny and host diversity in the coelomycetes Phomopsis. Can J Bot 72:166-167
59. Rocha ACS, Garcia D, Uetanabaro APT, Carneiro RTO, Isabela S, Araújo IS, Carlos Mattos CRR, Góes-Neto A (2011) Foliar endophytic fungi from Hevea brasiliensis and their antagonism on Microcyclus ulei. Fungal Divers 47:75-84
60. Rokas A, Williams BL, King N, Carroll SB (2003a) Genome scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804
61. Rokas A, King N, Finnerty JR, Carroll SB (2003b) Conflicting phylogenetic signals at the base of the metazoan tree. Dev Evol 5:346-359
62. Rossman AY, Farr DF, Castlebury LA (2007) A review of the phylogeny and biology of the Diaporthales. Mycoscience 48:135-144
63. Santos JM, Phillips AJL (2009) Resolving the complex of Diaporthe (Phomopsis) species occurring on Foeniculum vulgare in Portugal. Fungal Divers 34:111-125
64. Santos JM, Correia VG, Phillips AJL (2010) Primers for mating-type diagnosis in Diaporthe and Phomopsis: their use in teleomorph induction in vitro and biological species definition. Fungal Biol 114:255-270
65. Santos JM, Vrandečić K, C̈osić J, Duvnjak T, Phillips AJL (2011) Resolving the Diaporthe species occurring on soybean in Croatia. Persoonia 27:9-19
66. Schmitt I, Crespo A, Divakar PK, Fankhauser JD, Herman-Sackett E, Kalb K, Nelsen MP, Nelson NA, Rivas-Plata E, Shimp AD, Widhelm T, Lumbsch HT (2009) New primers for promising single copy genes in fungal phylogenetics and systematic. Persoonia 23:35-40
67. Schoch CL, Shoemaker RA, Seifert KA, Hambleton S, Spatafora JW, Crous PW (2006) A multigene phylogeny of the Dothideomycetes using four nuclear loci. Mycologia 98:1041-1052
68. Schoch CL, Seifert KA, Huhndorf S et al (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. P Natl Acad Sci 109:6241-6246
69. Shivas RG, Cai L (2011) Cryptic fungal species unmasked. Microbiology Australia 33:36-37
70. Summerell BA, Leslie JF (2011) Fifty years of Fusarium: how were nine species ever enough? Fungal Divers 50:135-144
71. Summerell BA, Laurence MH, Liew ECY, Leslie JF (2010) Biogeography and phylogeography of Fusarium: a review. Fungal Divers 44:3-13
72. Sun X, Guo LD, Hyde KD (2011) Community composition of endophytic fungi in Acer truncatum and their role in decomposition. Fungal Divers 47:85-95
73. Sun S, Van K, Kim MY, Min KH, Lee YW, Lee SH (2012) Diaporthe phaseolorum var. caulivora, a causal agent for both stem canker and seed decay on soybean. Plant Pathol J 28:55-59
74. Sutton DA, Timm WD, Morgan-Jones G, Rinaldi MG (1999) Human phaeohyphomycotic osteomyelitis caused by the coelomycete Phomopsis Saccardo 1905: criteria for identification, case history, and therapy. J Clin Microbiol 37:807-811
75. Swofford DL (2002) PAUP 4.0b10: phylogenetic analysis using parsimony. Sinauer Associates, Sunderland
76. Taylor JW, Jacobson DJ, Kroken S, Kasuga T, Geiser DM, Hibbett DS, Fisher MC (2000) Phylogenetic species recognition and species concepts in fungi. Fungal Genet Biol 31:21-32
77. Templeton AR (1989) The meaning of species and speciation: a genetic perspective. In: Otte D, Endler JA (eds) Speciation and its consequences. Sinauer, Sunderland, pp 3-27
78. Thompson JD, Higgins DG, Gibson TJ (1994) ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
79. Thompson SM, Tan YP, Young AJ, Neate SM, Aitken EA, Shivas RG (2011) Stem cankers on sunflower (Helianthus annuus) in Australia reveal a complex of pathogenic Diaporthe (Phomopsis) species. Persoonia 27:80-89
80. Udayanga D, Liu XX, McKenzie EHC, Chukeatirote E, Bahkali AH, Hyde KD (2011) The genus Phomopsis: biology, applications, species concepts and names of common phytopathogens. Fungal Divers 50:189-225
81. Udayanga D, Liu XX, Crous PW, McKenzie EHC, Chukeatirote E, Hyde KD (2012) Multilocus phylogeny of Diaporthe reveals three new cryptic species from Thailand. Cryptogamie Mycologie. In Press
82. Uecker FA (1988) A world list of Phomopsis names with notes on nomenclature, morphology and biology. Mycol Mem 13:1-231
83. van der Aa HA, Noordeloos ME, Gruyter J (1990) Species concepts in some larger genera of the coelomycetes. Stud Mycol 32:3-19
84. van Niekerk JM, Groenewald JZ, Farr DF, Fourie PH, Halleen F, Crous PW (2005) Reassessment of Phomopsis species on grapevine. Australas Plant Path 34:27-39
85. van Rensburg JCJ, Lamprecht SC, Groenewald JZ, Castlebury LA, Crous PW (2006) Characterisation of Phomopsis spp. associated with die-back of rooibos (Aspalathus linearis) in South Africa. Stud Mycol 55:65-74
86. van Warmelo KT, Marasas WFO, Adelaar TF, Kellerman TS, van Rensburg IBJ, Minne JA (1970) Experimental evidence that lupinosis of sheep is a mycotoxicosis caused by the fungus Phomopsis leptostromiformis (Kuhn) Bubak. J S Afr Vet Med Assoc 41:235-247
87. Walker DM, Castlebury LA, Rossman AY, White JF (2012) New molecular markers for fungal phylogenetics: two genes for species level systematics in the Sordariomycetes (Ascomycota). Molecular Phylogenetics and Evolution. Accepted. Manuscript MPE-11-256
88. Wang XH, Chen GQ, Huang F, Zhang JZ, Hyde KD, Li HG (2011) Phyllosticta species associated with citrus diseases in China. Fungal Divers 52:209-224
89. Wehmeyer LE (1933) The genus Diaporthe Nitschke and its segregates. University of Michigan Studies Scientific Series 9:1-34
90. White TJ, Bruns T, Lee S, Taylor JW (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. New York Academic Press. pp 315-322
91. Wikee S, Udayanga D, Crous PW, McKenzie EHC, Chukeatirote E, Bahkali AH, Hyde KD (2011) Phyllostica- an overview of current status of species recognition. Fungal Divers 51:46-60
92. Wingfield MJ, de Beer ZW, Slippers B, Wingfield BD, Groenewald JZ, Lombard L, Crous PW (2012) One fungus one name promotes progressive plant pathology. Molecular Plant Pathology 13:604-613
93. Wu ZH, Wang TH, Huang W, Qu YB (2001) A simplified method for chromosome DNA preparation from filamentous fungi. Mycosystema 20:575-577
94. Zhang N (2002) Molecular phylogeny of Melanospora and Diaporthales, and population genetics of dogwood anthracnose fungus. PhD Thesis. Department of Biological Sciences, Lousiana State University
95. Zhang AW, Hartman GL, Riccioni L, Chen WD, Ma RZ, Pedersen WL (1997) Using PCR to distinguish Diaporthe phaseolorum and Phomopsis longicolla from other soybean fungal pathogens and to detect them in soybean tis-sues. Plant Dis 81:1143-1149
96. Zhang AW, Riccioni L, Pedersen WL, Kollipara KP, Hartman GL (1998) Molecular identification and phylogenetic grouping of Diaporthe phaseolorum and Phomopsis longicolla isolates from soybean. Phytopathology 88:1306-1314