The Genomes of the Fungal Plant Pathogens and Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry

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We sequenced and compared the genomes of the Dothideomycete fungal plant pathogens Cladosporium fulvum (Cfu) (syn. Passalora fulva) and Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles and hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse is a hemibiotroph infecting pine. The genomes of these fungi have a similar set of genes (70% of gene content in both genomes are homologs), but differ significantly in size (Cfu >61.1-Mb; Dse 31.2-Mb), which is mainly due to the difference in repeat content (47.2% in Cfu versus 3.2% in Dse). Recent adaptation to different lifestyles and hosts is suggested by diverged sets of genes. Cfu contains an α-tomatinase gene that we predict might be required for detoxification of tomatine, while this gene is absent in Dse. Many genes encoding secreted proteins are unique to each species and the repeat-rich areas in Cfu are enriched for these species-specific genes. In contrast, conserved genes suggest common host ancestry. Homologs of Cfu effector genes, including Ecp2 and Avr4, are present in Dse and induce a Cf-Ecp2- and Cf-4-mediated hypersensitive response, respectively. Strikingly, genes involved in production of the toxin dothistromin, a likely virulence factor for Dse, are conserved in Cfu, but their expression differs markedly with essentially no expression by Cfu in planta. Likewise, Cfu has a carbohydrate-degrading enzyme catalog that is more similar to that of necrotrophs or hemibiotrophs and a larger pectinolytic gene arsenal than Dse, but many of these genes are not expressed in planta or are pseudogenized. Overall, comparison of their genomes suggests that these closely related plant pathogens had a common ancestral host but since adapted to different hosts and lifestyles by a combination of differentiated gene content, pseudogenization, and gene regulation.

Vyšlo v časopise: The Genomes of the Fungal Plant Pathogens and Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry. PLoS Genet 8(11): e32767. doi:10.1371/journal.pgen.1003088
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003088

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Zdroje

1. van KanJAL, van den AckervekenGFJM, de WitPJGM (1991) Cloning and characterization of cDNA of avirulence gene Avr9 of the fungal pathogen Cladosporium fulvum, causal agent of tomato leaf mold. Mol Plant-Microbe Interact 4: 52–59.

2. ThommaBPHJ, Van EsseHP, CrousPW, De WitPJGM (2005) Cladosporium fulvum (syn. Passalora fulva), a highly specialized plant pathogen as a model for functional studies on plant pathogenic Mycosphaerellaceae. Mol Plant Pathol 6: 379–393.

3. GoodwinSB, DunkleLD, ZismannVL (2001) Phylogenetic analysis of Cercospora and Mycosphaerella based on the internal transcribed spacer region of ribosomal DNA. Phytopathology 91: 648–658.

4. BradshawRE, ZhangSG (2006) Biosynthesis of dothistromin. Mycopathologia 162: 201–213.

5. BarnesI, CrousPW, WingfieldBD, WingfieldMJ (2004) Multigene phylogenies reveal that red band needle blight of Pinus is caused by two distinct species of Dothistroma, D. septosporum and D. pini. Stud Mycol 50: 551–565.

6. JenkinsJA (1948) The origin of the cultivated tomato. Econ Bot 2: 379–392.

7. CookeMC (1883) New American fungi. Grevillea XII: 32.

8. De WitPJGM (1992) Molecular characterization of gene-for-gene systems in plant-fungus interactions and the application of avirulence genes in control of plant-pathogens. Annu Rev Phytopathol 30: 391–418.

9. EnyaJ, IkedaK, TakeuchiT, HorikoshiN, HigashiT, et al. (2009) The first occurrence of leaf mold of tomato caused by races 4.9 and 4.9.11 of Passalora fulva (syn. Fulvia fulva) in Japan. J Gen Plant Pathol 75: 76–79.

10. IidaY, IwadateY, KubotaM, TeramiF (2010) Occurrence of a new race 2.9 of leaf mold of tomato in Japan. J Gen Plant Pathol 76: 84–86.

11. BednarovaM, PalovcikovaD, JankovskyL (2006) The host spectrum of Dothistroma needle blight Mycosphaerella pini E. Rostrup - new hosts of Dothistroma needle bight observed in the Czech Republic. J For Sci 52: 30–36.

12. BradshawRE (2004) Dothistroma (red-band) needle blight of pines and the dothistromin toxin: a review. For Pathol 34: 163–185.

13. WoodsAJ, CoatesKD, HamannA (2005) Is an unprecedented Dothistroma needle blight epidemic related to climate change? Bioscience 55: 761–769.

14. Brown A, Webber JF (2008) Red band needle blight of conifers in Britain. Edinburgh, UK: Forestry Commission. 1–8 p.

15. WoodsA (2011) Is the health of British Columbia's forests being influenced by climate change? If so, was this predictable? Can J Plant Pathol 33: 117–126.

16. LazarovitsG, HigginsVJ (1976) Ultrastucture of susceptible, resistant and immune reactions of tomato to races of Cladosporium fulvum. Can J Bot 54: 235–249.

17. LazarovitsG, HigginsVJ (1976) Histological comparison of Cladosporium fulvum race 1 on immune, resistant and susceptible tomato varieties. Can J Bot 54: 224–234.

18. De WitPJGM (1977) A light and scanning-electron microscopic study of the infection of tomato plants by virulent and avirulent races of Cladosporium fulvum. Neth J Plant Pathol 83: 109–122.

19. MuirJA, CobbJFW (2005) Infection of radiata and bishop pine by Mycosphaerella pini in California. Can J For Res 35: 2529–2538.

20. GadgilPD (1967) Infection of Pinus radiata needles by Dothistroma pini. N Z J Bot 5: 498–503.

21. StergiopoulosI, GroenewaldM, StaatsM, LindhoutP, CrousPW, et al. (2007) Mating-type genes and the genetic structure of a world-wide collection of the tomato pathogen Cladosporium fulvum. Fungal Genet Biol 44: 415–429.

22. GroenewaldM, BarnesI, BradshawRE, BrownAV, DaleA, et al. (2007) Characterization and distribution of mating type genes in the Dothistroma needle blight pathogens. Phytopathology 97: 825–834.

23. TomšovskýM, TomešováV, PalovčíkováD, KostovčíkM, RohrerM, et al. (2012) The gene flow and mode of reproduction of Dothistroma septosporum in the Czech Republic. Plant Pathol (In Press) DOI: 10.1111/j.1365-3059.2012.02625.x.

24. DaleAL, LewisKJ, MurrayBW (2011) Sexual Reproduction and Gene Flow in the Pine Pathogen Dothistroma septosporum in British Columbia. Phytopathology 101: 68–76.

25. HirstP, RichardsonTE, CarsonSD, BradshawRE (1999) Dothistroma pini genetic diversity is low in New Zealand. N Z J For Sci 29: 459–472.

26. JoostenMHAJ, De WitPJGM (1999) The tomato-Cladosporium fulvum interaction: A versatile experimental system to study plant-pathogen interactions. Annu Rev Phytopathol 37: 335–367.

27. De WitPJGM, JoostenMHAJ, ThommaBPHJ, StergiopoulosI (2009) Gene-for-gene models and beyond: the Cladosporium fulvum-tomato pathosystem. The Mycota V: 135–156.

28. De JongeR, Van EsseHP, KombrinkA, ShinyaT, DesakiY, et al. (2010) Conserved fungal LysM effector Ecp6 prevents chitin-triggered immunity in plants. Science 329: 953–955.

29. De KockMJD, BrandwagtBF, BonnemaG, De WitPJGM, LindhoutP (2005) The tomato Orion locus comprises a unique class of Hcr9 genes. Mol Breed 15: 409–422.

30. van EsseHP, BoltonMD, StergiopoulosI, de WitPJGM, ThommaBPHJ (2007) The chitin-binding Cladosporium fulvum effector protein Avr4 is a virulence factor. Mol Plant-Microbe Interact 20: 1092–1101.

31. van den BurgHA, HarrisonSJ, JoostenMHAJ, VervoortJ, de WitPJGM (2006) Cladosporium fulvum Avr4 protects fungal cell walls against hydrolysis by plant chitinases accumulating during infection. Mol Plant-Microbe Interact 19: 1420–1430.

32. StergiopoulosI, KourmpetisYAI, SlotJC, BakkerFT, De WitPJGM, et al. (2012) In silico characterization and molecular evolutionary analysis of a novel superfamily of fungal effector proteins. Mol Biol Evol 29: 3371–3384.

33. StergiopoulosI, Van den BurgHA, ÖkmenB, BeenenH, KemaGHJ, et al. (2010) Tomato Cf resistance proteins mediate recognition of cognate homologous effectors from fungi pathogenic on dicots and monocots. Proc Natl Acad Sci, USA 107: 7610–7615.

34. ShawGJ, ChickM, HodgesR (1978) A 13C-NMR study of the biosynthesis of the anthraquinone dothistromin by Dothistroma pini. Phytochemistry 17: 1743–1745.

35. SchwelmA, BarronNJ, BakerJ, DickM, LongPG, et al. (2009) Dothistromin toxin is not required for dothistroma needle blight in Pinus radiata. Plant Pathol 58: 293–304.

36. BradshawRE, JinHP, MorganBS, SchwelmA, TeddyOR, et al. (2006) A polyketide synthase gene required for biosynthesis of the aflatoxin-like toxin, dothistromin. Mycopathologia 161: 283–294.

37. SchwelmA, BarronNJ, ZhangS, BradshawRE (2008) Early expression of aflatoxin-like dothistromin genes in the forest pathogen Dothistroma septosporum. Mycol Res 112: 138–146.

38. ZhangS, SchwelmA, JinHP, CollinsLJ, BradshawRE (2007) A fragmented aflatoxin-like gene cluster in the forest pathogen Dothistroma septosporum. Fungal Genet Biol 44: 1342–1354.

39. SchwelmA, BradshawRE (2010) Genetics of dothistromin biosynthesis of Dothistroma septosporum: an update. Toxins 2: 2680–2698.

40. GrigorievIV, NordbergH, ShabalovI, AertsA, CantorM, et al. (2012) The genome portal of the Department of Energy Joint Genome Institute. Nucleic Acids Res 40: D26–32.

41. van der BurgtA, SeveringE, de WitP, CollemareJ (2012) Birth of new spliceosomal introns in fungi by multiplication of introner-like elements. Curr Biol 22: 1260–1265.

42. OhmRA, FeauN, HenrissatB, SchochCL, HorwitzBA, et al. (2012) Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathogens (In Press)..

43. AmselemJ, CuomoCA, van KanJAL, ViaudM, BenitoEP, et al. (2011) Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet 7: e1002230 doi:10.1371/journal.pgen.1002230.

44. SpanuPD, AbbottJC, AmselemJ, BurgisTA, SoanesDM, et al. (2010) Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism. Science 330: 1543–1546.

45. SchmidtSM, PanstrugaR (2011) Pathogenomics of fungal plant parasites: what have we learnt about pathogenesis? Curr Opin Plant Biol 14: 392–399.

46. PoulterRTM, GoodwinTJD, ButlerMI (2003) Vertebrate helentrons and other novel helitrons. Gene 313: 201–212.

47. KapitonovVV, JurkaJ (2007) Helitrons on a roll: eukaryotic rolling-circle transposons. Trends Genet 23: 521–529.

48. LambJC, TheuriJ, BirchlerJA (2004) What's in a centromere? Genome Biology 5: 239.

49. RoyB, SanyalK (2011) Diversity in requirement of genetic and epigenetic factors for centromere function in fungi. Eukaryot Cell 10: 1384–1395.

50. FreitagM, WilliamsRL, KotheGO, SelkerEU (2002) A cytosine methyltransferase homologue is essential for repeat-induced point mutation in Neurospora crassa. Proc Natl Acad Sci USA 99: 8802–8807.

51. HaneJK, LoweRGT, SolomonPS, TanKC, SchochCL, et al. (2007) Dothideomycete-plant interactions illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorum. Plant Cell 19: 3347–3368.

52. FudalI, RossS, BrunH, BesnardA-L, ErmelM, et al. (2009) Repeat-induced point mutation (RIP) as an alternative mechanism of evolution toward virulence in Leptosphaeria maculans. Mol Plant-Microbe Interact 22: 932–941.

53. GoutL, FudalI, KuhnML, BlaiseF, EckertM, et al. (2006) Lost in the middle of nowhere: the AvrLm1 avirulence gene of the Dothideomycete Leptosphaeria maculans. Mol Microbiol 60: 67–80.

54. RouxelT, GrandaubertJ, HaneJK, HoedeC, van de WouwAP, et al. (2011) Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations. Nat Commun 2: 202.

55. NowrousianM, StajichJE, ChuM, EnghI, EspagneE, et al. (2010) De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis. PLoS Genet 6: e1000891 doi:10.1371/journal.pgen.1000891.

56. HaneJK, RouxelT, HowlettBJ, KemaGHJ, GoodwinSB, et al. (2011) A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi. Genome Biol 12: R45.

57. ThonMR, PanHQ, DienerS, PapalasJ, TaroA, et al. (2006) The role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae. Genome Biol 7: R16.

58. StergiopoulosI, De WitPJGM (2009) Fungal effector proteins. Annu Rev Phytopathol 47: 233–263.

59. GoodwinSB, Ben M'BarekS, DhillonB, WittenbergAHJ, CraneCF, et al. (2011) Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis. PLoS Genet 7: e1002070 doi:10.1371/journal.pgen.1002070.

60. RivasS, ThomasCM (2005) Molecular interactions between tomato and the leaf mold pathogen Cladosporium fulvum. Annu Rev Phytopathol 43: 395–436.

61. WilcoxPL, AmersonHV, KuhlmanEG, LiuBH, O'MalleyDM, et al. (1996) Detection of a major gene for resistance to fusiform rust disease in loblolly pine by genomic mapping. Proc Natl Acad Sci USA 93: 3859–3864.

62. LiuJJ, EkramoddoullahAKM (2011) Genomic organization, induced expression and promoter activity of a resistance gene analog (PmTNL1) in western white pine (Pinus monticola). Planta 233: 1041–1053.

63. NelsonCD, KubisiakTL, AmersonHV (2010) Unravelling and managing fusiform rust disease: a model approach for coevolved forest tree pathosystems. For Pathol 40: 64–72.

64. van den AckervekenGFJM, van KanJAL, de WitPJGM (1992) Molecular analysis of the avirulence gene Avr9 of the fungal tomato pathogen Cladosporium fulvum fully supports the gene-for-gene hypothesis. Plant J 2: 359–366.

65. ChumaI, IsobeC, HottaY, IbaragiK, FutamataN, et al. (2011) Multiple translocation of the AVR-Pita effector gene among chromosomes of the rice blast fungus Magnaporthe oryzae and related species. PLoS Pathog 7: e1002147 doi:10.1371/journal.ppat.1002147.

66. WesterinkN, BrandwagtBF, De WitPJGM, JoostenMHAJ (2004) Cladosporium fulvum circumvents the second functional resistance gene homologue at the Cf-4 locus (Hcr9-4E) by secretion of a stable avr4E isoform. Mol Microbiol 54: 533–545.

67. LaugéR, GoodwinPH, De WitPJGM, JoostenMHAJ (2000) Specific HR-associated recognition of secreted proteins from Cladosporium fulvum occurs in both host and non-host plants. Plant J 23: 735–745.

68. WesselsJGH (1994) Developmental regulation of fungal cell-wall formation. Annu Rev Phytopathol 32: 413–437.

69. TempletonMD, RikkerinkEHA, BeeverRE (1994) Small, cysteine-rich proteins and recognition in fungal-plant interactions. Mol Plant-Microbe Interact 7: 320–325.

70. JoostenMHAJ, VerbakelHM, NettekovenME, van LeeuwenJ, van der VossenRTM, et al. (2005) The phytopathogenic fungus Cladosporium fulvum is not sensitive to the chitinase and β-1,3-glucanase defence proteins of its host, tomato. Physiol Mol Plant Pathol 46: 45–59.

71. SpanuP (1997) HCF-1, a hydrophobin from the tomato pathogen Cladosporium fulvum. Gene 193: 89–96.

72. WhitefordJR, SpanuPD (2001) The hydrophobin HCf-1 of Cladosporium fulvum is required for efficient water-mediated dispersal of conidia. Fungal Genet Biol 32: 159–168.

73. LacroixH, WhitefordJR, SpanuPD (2008) Localization of Cladosporium fulvum hydrophobins reveals a role for HCf-6 in adhesion. FEMS Microbiol Lett 286: 136–144.

74. CantarelBL, CoutinhoPM, RancurelC, BernardT, LombardV, et al. (2009) The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res 37: D233–238.

75. MartinezD, BerkaRM, HenrissatB, SaloheimoM, ArvasM, et al. (2008) Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol 26: 553–560.

76. PutoczkiTL, GerrardJA, ButterfieldBG, JacksonSL (2008) The distribution of un-esterified and methyl-esterified pectic polysaccharides in Pinus radiata. IAWA Journal 29: 115–127.

77. RidleyBL, O'NeillMA, MohnenDA (2001) Pectins: structure, biosynthesis, and oligogalacturonide-related signaling. Phytochemistry 57: 929–967.

78. SprockettDD, PiontkivskaH, BlackwoodCB (2011) Evolutionary analysis of glycosyl hydrolase family 28 (GH28) suggests lineage-specific expansions in necrotrophic fungal pathogens. Gene 479: 29–36.

79. Ten HaveA, MulderW, VisserJ, van KanJAL (1998) The endopolygalacturonase gene Bcpg1 is required for full virulence of Botrytis cinerea. Mol Plant-Microbe Interact 11: 1009–1016.

80. van KanJAL (2006) Licensed to kill: the lifestyle of a necrotrophic plant pathogen. Trends Plant Sci 11: 247–253.

81. EastwoodDC, FloudasD, BinderM, MajcherczykA, SchneiderP, et al. (2011) The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi. Science 333: 762–765.

82. OhmRA, de JongJF, LugonesLG, AertsA, KotheE, et al. (2010) Genome sequence of the model mushroom Schizophyllum commune. Nat Biotechnol 28: 957–U910.

83. van den BrinkJ, de VriesRP (2011) Fungal enzyme sets for plant polysaccharide degradation. Appl Microbiol Biotechnol 91: 1477–1492.

84. LeeMH, ChiuCM, RoubtsovaT, ChouCM, BostockRM (2010) Overexpression of a redox-regulated cutinase gene, MfCUT1, increases virulence of the brown rot pathogen Monilinia fructicola on Prunus spp.. Mol Plant-Microbe Interact 23: 176–186.

85. SkamniotiP, GurrSJ (2008) Cutinase and hydrophobin interplay: A herald for pathogenesis? Plant Signal Behav 3: 248–250.

86. KingBC, WaxmanKD, NenniNV, WalkerLP, BergstromGC, et al. (2011) Arsenal of plant cell wall degrading enzymes reflects host preference among plant pathogenic fungi. Biotechnol Biofuels 4: 4.

87. de VriesRP, BurgersK, van de VondervoortPJI, FrisvadJC, SamsonRA, et al. (2004) A new black Aspergillus species, A. vadensis, is a promising host for homologous and heterologous protein production. Appl Environ Microbiol 70: 3954–3959.

88. CoutinhoPM, AndersenMR, KolenovaK, vanKuykPA, BenoitI, et al. (2009) Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and comparison to Aspergillus niger and Aspergillus oryzae. Fungal Genet Biol 46: S161–S169.

89. BergB, DeantaRC, EscuderoA, GardenasA, JohanssonMB, et al. (1995) The chemical composition of newly shed needle litter of scots pine and some other pine species in a climatic transect. X. Long-term decomposition in a scots pine forest. Can J Bot 73: 1423–1435.

90. VogelJ (2008) Unique aspects of the grass cell wall. Curr Opin Plant Biol 11: 301–307.

91. Pareja-JaimeY, RonceroMIG, Ruiz-RoldánMC (2008) Tomatinase from Fusarium oxysporum f. sp. lycopersici is required for full virulence on tomato plants. Mol Plant-Microbe Interact 21: 728–736.

92. BartheGA, JourdanPS, McIntoshCA, MansellRL (1988) Radioimmunoassay for the quantitative determination of hesperidin and analysis of its distribution in Citrus sinensis. Phytochemistry 27: 249–254.

93. DiGuistiniS, WangY, LiaoNY, TaylorG, TanguayP, et al. (2011) Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen. Proc Natl Acad Sci USA 108: 2504–2509.

94. HammerschmidtR, BonnenAM, BergstromGC (1983) Association of lignification with non-host resistance of cucurbits. Phytopathology 73: 829–829.

95. XuL, ZhuL, TuL, LiuL, YuanD, et al. (2011) Lignin metabolism has a central role in the resistance of cotton to the wilt fungus Verticillium dahliae as revealed by RNA-Seq-dependent transcriptional analysis and histochemistry. J Exp Bot 62: 5607–5621.

96. BergB, WessenB, EkbohmG (1982) Nitrogen level and decomposition in scots pine needle litter. Oikos 38: 291–296.

97. LukjanovaA, MandreM (2008) Anatomical structure and localisation of lignin in needles and shoots of Scots pine (Pinus sylvestris L.) growing in a habitat with varying environmental characteristics. For Stud 49: 37–46.

98. KirkTK, FarrellRL (1987) Enzymatic “combustion”: the microbial degradation of lignin. Annu Rev Microbiol 41: 465–505.

99. Ruiz-DueñasFJ, MartínezAT (2009) Microbial degradation of lignin: how a bulky recalcitrant polymer is efficiently recycled in nature and how we can take advantage of this. Microb Biotechnol 2: 164–177.

100. Collemare J, Lebrun M-H (2012) Fungal secondary metabolites: ancient toxins and novel effectors in plant-microbe interactions. In: Martin F, Kamoun S, editors. Effectors in Plant-Microbe Interactions: Blackwell Publishing Ltd. pp. 379–402.

101. DaviesDG, HodgeP (1974) Chemistry of quinones. 5. Structure of cladofulvin, a bianthraquinone from Cladosporium fulvum Cooke. J Chemi Soc-Perkin Trans 1: 2403–2405.

102. BradshawRE, BhatnagarD, GanleyRJ, GillmanCJ, MonahanBJ, et al. (2002) Dothistroma pini, a forest pathogen, contains homologs of aflatoxin biosynthetic pathway genes. Appl Environ Microbiol 68: 2885–2892.

103. KellerNP, HohnTM (1997) Metabolic pathway gene clusters in filamentous fungi. Fungal Genet Biol 21: 17–29.

104. KellerNP, TurnerG, BennettJW (2005) Fungal secondary metabolism - From biochemistry to genomics. Nat Rev Microbiol 3: 937–947.

105. CollemareJ, BillardA, BoehnertHU, LebrunMH (2008) Biosynthesis of secondary metabolites in the rice blast fungus Magnaporthe grisea: the role of hybrid PKS-NRPS in pathogenicity. Mycol Res 112: 207–215.

106. GalaganJE, CalvoSE, CuomoC, MaLJ, WortmanJR, et al. (2005) Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438: 1105–1115.

107. CuomoCA, GueldenerU, XuJ-R, TrailF, TurgeonBG, et al. (2007) The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science 317: 1400–1402.

108. KhaldiN, WolfeKH (2011) Evolutionary origins of the fumonisin secondary metabolite gene cluster in Fusarium verticillioides and Aspergillus niger. Int J Evol Biol 2011: 423821.

109. YangZ, BielawskiJP (2000) Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15: 496–503.

110. EhrlichKC, YuJJ, CottyPJ (2005) Aflatoxin biosynthesis gene clusters and flanking regions. J Appl Microbiol 99: 518–527.

111. BergmannS, FunkAN, ScherlachK, SchroeckhV, ShelestE, et al. (2010) Activation of a silent fungal polyketide biosynthesis pathway through regulatory cross talk with a cryptic nonribosomal peptide synthetase gene cluster. Appl Environ Microbiol 76: 8143–8149.

112. BrakhageAA, SchroeckhV (2011) Fungal secondary metabolites - Strategies to activate silent gene clusters. Fungal Genet Biol 48: 15–22.

113. BayramO, BrausGH (2011) Coordination of secondary metabolism and development in fungi: The velvet family of proteins. FEMS Microbiol Rev 35: 1–24.

114. TsitsigiannisDI, KellerNP (2006) Oxylipins act as determinants of natural product biosynthesis and seed colonisation in Aspergillus nidulans. Mol Microbiol 59: 882–892.

115. AdamsTH, BoylanMT, TimberlakeWE (1988) BrlA is necessary and sufficient to direct conidiophore development in Aspergillus nidulans. Cell 54: 353–362.

116. EnrightAJ, Van DongenS, OuzounisCA (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30: 1575–1584.

117. KatohK, TohH (2008) Recent developments in the MAFFT multiple sequence alignment program. Briefings Bioinf 9: 286–298.

118. StamatakisA, HooverP, RougemontJ (2008) A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 57: 758–771.

119. BaoZR, EddySR (2002) Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res 12: 1269–1276.

120. Smit AFA, Hubley R, Green P (1996–2010) RepeatMasker Open-3.0. Available: http://www.repeatmasker.org. Accessed 12 December 2011.

121. LewisZA, HondaS, KhlafallahTK, JeffressJK, FreitagM, et al. (2009) Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa. Genome Res 19: 427–437.

122. DelcherAL, SalzbergSL, PhillippyAM (2003) Using MUMmer to identify similar regions in large sequence sets. Curr Protoc Bioinf 10.3.1–10.3.18.

123. ParkJ, ParkB, JungK, JangS, YuK, et al. (2008) CFGP: a web-based, comparative fungal genomics platform. Nucleic Acids Res 36: D562–D571.

124. HortonP, ParkK-J, ObayashiT, FujitaN, HaradaH, et al. (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res 35: W585–W587.

125. BendtsenJD, NielsenH, von HeijneG, BrunakS (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783–795.

126. KaellL, KroghA, SonnhammerELL (2007) Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server. Nucleic Acids Res 35: W429–W432.

127. KroghA, LarssonB, von HeijneG, SonnhammerELL (2001) Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J Mol Biol 305: 567–580.

128. EmanuelssonO, NielsenH, BrunakS, von HeijneG (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 300: 1005–1016.

129. PierleoniA, MartelliPL, CasadioR (2008) PredGPI: a GPI-anchor predictor. BMC Bioinformatics 9: 392.

130. van der HoornRAL, LaurentF, RothR, de WitPJGM (2000) Agroinfiltration is a versatile tool that facilitates comparative analyses of Avr9/Cf-9-induced and Avr4/Cf-4-induced necrosis. Mol Plant-Microbe Interact 13: 439–446.

131. Hammond-KosackKE, StaskawiczBJ, JonesJDG, BaulcombeDC (1995) Functional expression of a fungal avirulence gene from a modified Potato-Virus-X genome. Mol Plant-Microbe Interact 8: 181–185.

132. KarimiM, InzeD, DepickerA (2002) GATEWAY vectors for Agrobacterium-mediated plant transformation. Trends Plant Sci 7: 193–195.

133. WhitefordJR, SpanuPD (2002) Hydrophobins and the interactions between fungi and plants. Mol Plant Pathol 3: 391–400.

134. TamuraK, PetersonD, PetersonN, StecherG, NeiM, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731–2739.

135. WernerssonR, PedersenAG (2003) RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences. Nucl Acids Res 31: 3537–3539.

136. WaterhouseAM, ProcterJB, MartinDMA, ClampM, BartonGJ (2009) Jalview version 2 — a multiple sequence alignment editor and analysis workbench. Bioinformatics 25: 1189–1191.

137. ZhangZ, LiJ, ZhaoXQ, WangJ, WongGK, et al. (2006) KaKs Calculator: Calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinf 4: 259–263.

138. NeiM, GojoboriT (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3: 418–426.

139. Student (1908) The probable error of a mean. Biometrika 6: 1–25.

140. ChettriP, CalvoAM, CaryJW, DhingraS, GuoYA, et al. (2012) The veA gene of the pine needle pathogen Dothistroma septosporum regulates sporulation and secondary metabolism. Fungal Genet Biol 49: 141–151.

141. GamborgOL, MillerRA, OjimaK (1968) Nutrient requirements of suspension cultures of soybean root cell. Exp Cell Res 50: 151–158.

142. van EsseHP, Van 't KloosterJW, BoltonMD, YadetaKA, van BaarlenP, et al. (2008) The Cladosporium fulvum virulence protein Avr2 inhibits host proteases required for basal defense. Plant Cell 20: 1948–1963.

143. UntergasserA, NijveenH, RaoX, BisselingT, GeurtsR, et al. (2007) Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 35: W71–75.

144. LivakKJ, SchmittgenTD (2001) Analysis of relative gene expression data using real time quantitative PCR and the 2−ΔΔCT method. Methods 25: 402–408.