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Evolution and genome architecture in fungal plant pathogens

Möller, Mareike, Stukenbrock, Eva H.·2017·Nature Reviews Microbiology
DOI 10.1038/nrmicro.2017.76
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  1. James, T. Y. et al. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443, 818–822 (2006). · DOI
  2. Lo Presti, L. et al. Fungal effectors and plant susceptibility. Annu. Rev. Plant Biol. 66, 513–545 (2015). · DOI · Paper page
  3. Wolpert, T. J., Dunkle, L. D. & Ciuffetti, L. M. Host-selective toxins and avirulence determinants: what's in a name? Annu. Rev. Phytopathol. 40, 251–285 (2002). · DOI · Paper page
  4. Friesen, T. L., Faris, J. D., Solomon, P. S. & Oliver, R. P. Host-specific toxins: effectors of necrotrophic pathogenicity. Cell. Microbiol. 10, 1421–1428 (2008). · DOI · Paper page
  5. Javelle, M., Vernoud, V., Rogowsky, P. M. & Ingram, G. C. Epidermis: the formation and functions of a fundamental plant tissue. New Phytol. 189, 17–39 (2011). · DOI · Paper page
  6. Weiberg, A. et al. Fungal small RNAs suppress plant immunity by hijacking host RNA interference pathways. Science 342, 118–123 (2013). · DOI
  7. Manning, V. A. & Ciuffetti, L. M. Localization of Ptr ToxA produced by Pyrenophora tritici-repentis reveals protein import into wheat mesophyll cells. Plant Cell 17, 3203–3212 (2005). · DOI
  8. Djamei, A. et al. Metabolic priming by a secreted fungal effector. Nature 478, 395–398 (2011). · DOI
  9. Bergelson, J., Kreitman, M., Stahl, E. A. & Tian, D. Evolutionary dynamics of plant R-genes. Science 292, 2281–2285 (2001). · DOI
  10. Barrett, L. G. et al. Diversity and evolution of effector loci in natural populations of the plant pathogen Melampsora lini. Mol. Biol. Evol. 26, 2499–2513 (2009). · DOI
  11. Dodds, P. N. et al. Direct protein interaction underlies gene-for-gene specificity and coevolution of the flax resistance genes and flax rust avirulence genes. Proc. Natl Acad. Sci. USA 103, 8888–8893 (2006). · DOI · Paper page
  12. Kanzaki, H. et al. Arms race co-evolution of Magnaporthe oryzae AVR-Pik and rice Pik genes driven by their physical interactions. Plant J. 72, 894–907 (2012). · DOI · Paper page
  13. Stukenbrock, E. H. et al. The making of a new pathogen: Insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species. Genome Res. 21, 2157–2166 (2011). · DOI
  14. de Jonge, R. et al. Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen. Genome Res. 23, 1271–1282 (2013). · DOI · Paper page
  15. Menardo, F. et al. Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species. Nat. Genet. 48, 201–205 (2016). This study provides an example of rapid adaptation to new host plants. The hybridization of two Blumeria graminis formae speciales resulted in the emergence of a new pathogen that infects a hybrid crop of wheat and rye. · DOI
  16. Selmecki, A., Forche, A. & Berman, J. Genomic plasticity of the human fungal pathogen Candida albicans. Eukaryot. Cell 9, 991–1008 (2010). · DOI · Paper page
  17. Farrer, R. A. et al. Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage. Proc. Natl Acad. Sci. USA 108, 18732–18736 (2011). · DOI · Paper page
  18. Raffaele, S. & Kamoun, S. Genome evolution in filamentous plant pathogens: why bigger can be better. Nat. Rev. Microbiol. 10, 417–430 (2012). · DOI · Paper page
  19. Seidl, M. F. & Thomma, B. P. Sex or no sex: evolutionary adaptation occurs regardless. Bioessays 36, 335–345 (2014). · DOI
  20. Galazka, J. M. & Freitag, M. Variability of chromosome structure in pathogenic fungi — of 'ends and odds'. Curr. Opin. Microbiol. 20, 19–26 (2014). · DOI
  21. Allen, R. L. et al. Host–parasite coevolutionary conflict between Arabidopsis and Downy Mildew. Science 306, 1957–1960 (2004). · DOI · Paper page
  22. Cao, J. et al. Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat. Genet. 43, 956–963 (2011). · DOI · Paper page
  23. Thrall, P. H. et al. Rapid genetic change underpins antagonistic coevolution in a natural host–pathogen metapopulation. Ecol. Lett. 15, 425–435 (2012). · DOI
  24. Laine, A.-L., Burdon, J. J., Nemri, A. & Thrall, P. H. Host ecotype generates evolutionary and epidemiological divergence across a pathogen metapopulation. Proc. R. Soc. B Biol. Sci. 281, 20140522 (2014). · DOI
  25. Persoons, A. et al. The escalatory Red Queen: population extinction and replacement following arms-race dynamics in poplar rust. Mol. Ecol. 26, 1902–1918 (2016). · DOI
  26. Daverdin, G. et al. Genome structure and reproductive behaviour influence the evolutionary potential of a fungal phytopathogen. PLoS Pathog. 8, e1003020 (2012). · DOI
  27. Rouxel, T. et al. Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations. Nat. Commun. 2, 202 (2011). · DOI
  28. Brown, J. K. & Hovmøller, M. S. Aerial dispersal of pathogens on the global and continental scales and its impact on plant disease. Science 297, 537–541 (2002). · DOI · Paper page
  29. Islam, M. T. et al. Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae. BMC Biol. 14, 84 (2016). · DOI
  30. Castroagudin, V. L. et al. Wheat blast disease caused by Pyricularia graminis-tritici sp. nov. Preprint at bioRxiv http://dx.doi.org/10.1101/051151 (2016). · DOI
  31. Brasier, C. M. Rapid evolution of introduced plant pathogens via interspecific hybridization. Bioscience 51, 123 (2001). · DOI
  32. Brasier, C. M. & Kirk, S. A. Rapid emergence of hybrids between the two subspecies of Ophiostoma novo-ulmi with a high level of pathogenic fitness. Plant Pathol. 59, 186–199 (2010). · DOI
  33. McDonald, B. A. & Stukenbrock, E. H. Rapid emergence of pathogens in agro-ecosystems: global threats to agricultural sustainability and food security. Phil. Trans. R. Soc. B 371, 20160026 (2016). · DOI · Paper page
  34. Stukenbrock, E. H. Evolution, selection and isolation: a genomic view of speciation in fungal plant pathogens. New Phytol. 199, 895–907 (2013). · DOI
  35. Brown, J. K. & Tellier, A. Plant–parasite coevolution: bridging the gap between genetics and ecology. Annu. Rev. Phytopathol. 49, 345–367 (2011). · DOI
  36. Hörger, A. C. et al. Balancing selection at the tomato RCR3 guardee gene family maintains variation in strength of pathogen defense. PLoS Genet. 8, e1002813 (2012). · DOI
  37. Tellier, A., Moreno-Gámez, S. & Stephan, W. Speed of adaptation and genomic footprints of host–parasite coevolution under arms race and trench warfare dynamics. Evolution. 68, 2211–2224 (2014).
  38. Van der Hoorn, R. A., De Wit, P. J. & Joosten, M. H. Balancing selection favors guarding resistance proteins. Trends Plant Sci. 7, 67–71 (2002). · DOI
  39. Badouin, H. et al. Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates. Mol. Ecol. 26, 2041–2062 (2016). · DOI
  40. Chuma, I. et al. Multiple translocation of the AVR-Pita effector gene among chromosomes of the rice blast fungus Magnaporthe oryzae and related species. PLoS Pathog. 7, e1002147 (2011). · DOI
  41. Ma, L.-J. et al. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464, 367–373 (2010). · DOI · Paper page
  42. Faino, L. et al. Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen. Genome Res. 26, 1091–1100 (2016). This study describes the importance of transposable elements in the formation of lineage-specific regions and their differential regulation in distinct genome compartments in V. dahliae. · DOI · Paper page
  43. Goodwin, S. B. et al. Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis. PLoS Genet. 7, e1002070 (2011). · DOI · Paper page
  44. Coleman, J. J. et al. The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genet. 5, e1000618 (2009). · DOI · Paper page
  45. Williams, A. H. et al. Comparative genomics and prediction of conditionally dispensable sequences in legume-infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors. BMC Genomics 17, 191 (2016). · DOI
  46. Dutheil, J. Y. et al. A tale of genome compartmentalization: the evolution of virulence clusters in smut fungi. Genome Biol. Evol. 8, 681–704 (2016). This study provides details of the evolution of virulence-associated gene clusters in S. scitamineum that are driven by tandem gene duplication and transposable elements. · DOI
  47. Dong, S., Raffaele, S. & Kamoun, S. The two-speed genomes of filamentous pathogens: waltz with plants. Curr. Opin. Genet. Dev. 35, 57–65 (2015). · DOI
  48. Stukenbrock, E. H. et al. Whole-genome and chromosome evolution associated with host adaptation and speciation of the wheat pathogen Mycosphaerella graminicola. PLoS Genet. 6, e1001189 (2010). · DOI
  49. Houben, A., Banaei-Moghaddam, A. M., Klemme, S. & Timmis, J. N. Evolution and biology of supernumerary B chromosomes. Cell. Mol. Life Sci. 71, 467–478 (2014). · DOI
  50. Miao, V. P., Covert, S. F. & VanEtten, H. D. A fungal gene for antibiotic resistance on a dispensable ('B') chromosome. Science 254, 1773 (1991). · DOI · Paper page
  51. Temporini, E. D. & VanEtten, H. D. Distribution of the pea pathogenicity (PEP) genes in the fungus Nectria haematococca mating population VI. Curr. Genet. 41, 107–114 (2002). · DOI
  52. van der Does, H. C. et al. Transcription factors encoded on core and accessory chromosomes of Fusarium oxysporum induce expression of effector genes. PLoS Genet. 12, e1006401 (2016). · DOI
  53. Wittenberg, A. H. J. et al. Meiosis drives extraordinary genome plasticity in the haploid fungal plant pathogen Mycosphaerella graminicola. PLoS ONE 4, e5863 (2009). · DOI
  54. Croll, D., Zala, M. & McDonald, B. A. Breakage–fusion–bridge cycles and large insertions contribute to the rapid evolution of accessory chromosomes in a fungal pathogen. PLoS Genet. 9, e1003567 (2013). · DOI
  55. Stewart, E. l. et al. Quantitative trait locus mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen Zymoseptoria tritici. Mol. Plant Pathol. http://dx.doi.org/10.1111/mpp.12515 (2017). · DOI
  56. Plissonneau, C. & Stürchler, A. The evolution of orphan regions in genomes of a fungal pathogen of wheat. mBio 7, e01231-16 (2016). In this study, comparison of the genome structure of two Z. tritici isolates identifies large chromosomal inversions and losses and/or gains of transposable element clusters, which highlights intraspecies genome diversity. · DOI
  57. Chiara, M. et al. Genome sequencing of multiple isolates highlights subtelomeric genomic diversity within Fusarium fujikuroi. Genome Biol. Evol. 7, 3062–3069 (2015). · DOI
  58. Soyer, J. L. et al. Epigenetic control of effector gene expression in the plant pathogenic fungus Leptosphaeria maculans. PLoS Genet. 10, e1004227 (2014). Effectors in L. maculans are located in AT-rich genome compartments. In this study, their regulation is shown to be mediated by the presence and absence of heterochromatin during infection. · DOI
  59. Schotanus, K. et al. Histone modifications rather than the novel regional centromeres of Zymoseptoria tritici distinguish core and accessory chromosomes. Epigenetics Chromatin 8, 1 (2015). In this study, Genome-wide comparison of histone methylation marks reveals distinct patterns of the facultative heterochromatin mark H3K27me3 on core and accessory chromosomes. · DOI
  60. Kellner, R. et al. Expression profiling of the wheat pathogen Zymoseptoria tritici reveals genomic patterns of transcription and host-specific regulatory programs. Genome Biol. Evol. 6, 1353–1365 (2014). · DOI
  61. Miao, V. P., Freitag, M. & Selker, E. U. Short TpA-rich segments of the ζ-η region induce DNA methylation in Neurospora crassa. J. Mol. Biol. 300, 249–273 (2000). · DOI
  62. Tamaru, H. & Selker, E. U. Synthesis of signals for de novo DNA methylation in Neurospora crassa. Mol. Cell. Biol. 23, 2379–2394 (2003). · DOI
  63. Fontanillas, E. et al. Degeneration of the non-recombining regions in the mating-type chromosomes of the anther-smut fungi. Mol. Biol. Evol. 32, 928–943 (2014). · DOI
  64. Kämper, J. et al. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis. Nature 444, 97–101 (2006). · DOI · Paper page
  65. Schirawski, J. et al. Pathogenicity determinants in smut fungi revealed by genome comparison. Science 330, 1546–1548 (2010). · DOI · Paper page
  66. Croll, D., Lendenmann, M. H., Stewart, E. & McDonald, B. A. The impact of recombination hotspots on genome evolution of a fungal plant pathogen. Genetics 201, 1213–1228 (2015). · DOI
  67. Ohm, R. A. et al. Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathog. 8, e1003037 (2012). · DOI · Paper page
  68. Hane, J. K. et al. A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi. Genome Biol. 12, 1 (2011). · DOI · Paper page
  69. Grandaubert, J. et al. Transposable element-assisted evolution and adaptation to host plant within the Leptosphaeria maculans–Leptosphaeria biglobosa species complex of fungal pathogens. BMC Genomics 15, 891 (2014). This study shows that the expansion of transposable elements in one member of the L. maculans–L. biglobosa species complex correlates to the evolution of pathogenicity in this species. · DOI
  70. Chang, T.-C. et al. Comparative genomics of the sigatoka disease complex on banana suggests a link between parallel evolutionary changes in Pseudocercospora fijiensis and Pseudocercospora eumusae and increased virulence on the banana host. PLoS Genet. 12, e1005904 (2016). · DOI
  71. Duplessis, S. et al. Obligate biotrophy features unraveled by the genomic analysis of rust fungi. Proc. Natl Acad. Sci. USA 108, 9166–9171 (2011). · DOI · Paper page
  72. Niehaus, E.-M. et al. Comparative 'omics' of the Fusarium fujikuroi species complex highlights differences in genetic potential and metabolite synthesis. Genome Biol. Evol. 8, 3574 (2016). · DOI
  73. Lynch, M. & Walsh, B. The origins of genome architecture (Sinauer Associates Sunderland, 2007).
  74. McDonald, B. A. & Linde, C. Pathogen population genetics, evolutionary potential, and durable resistance. Annu. Rev. Phytopathol. 40, 349–379 (2002). · DOI
  75. Marais, G. & Charlesworth, B. Genome evolution: recombination speeds up adaptive evolution. Curr. Biol. 13, R68–R70 (2003). · DOI
  76. Feldbrügge, M., Kämper, J., Steinberg, G. & Kahmann, R. Regulation of mating and pathogenic development in Ustilago maydis. Curr. Opin. Microbiol. 7, 666–672 (2004). · DOI
  77. Stukenbrock, E. H. & Dutheil, J. Y. Comparison of fine-scale recombination maps in fungal plant pathogens reveals dynamic recombination landscapes and intragenic hotspots. Preprint at bioRxiv https://dx.doi.org/10.1101/158907 (2017). · DOI
  78. Zheng, Y. et al. Development of microsatellite markers and construction of genetic map in rice blast pathogen Magnaporthe grisea. Fungal Genet. Biol. 45, 1340–1347 (2008). · DOI
  79. Talas, F. & McDonald, B. A. Genome-wide analysis of Fusarium graminearum field populations reveals hotspots of recombination. BMC Genomics 16, 996 (2015). This study provides details of the genomic structure of Fusarium graminearum field populations, which reveals a high degree of sexual recombination and gene flow that enables rapid adaptation to changing environments. · DOI
  80. Muller, H. J. Some genetic aspects of sex. Am. Nat. 66, 118–138 (1932). · DOI
  81. Taylor, J. W., Jacobson, D. J. & Fisher, M. C. The evolution of asexual fungi: reproduction, speciation and classification. Annu. Rev. Phytopathol. 37, 197–246 (1999). · DOI
  82. Milgroom, M. G., del Mar Jiménez-Gasco, M., García, C. O., Drott, M. T. & Jiménez-Díaz, R. M. Recombination between clonal lineages of the asexual fungus Verticillium dahliae detected by genotyping by sequencing. PLoS ONE 9, e106740 (2014). · DOI
  83. Short, D. P. G., Gurung, S., Hu, X., Inderbitzin, P. & Subbarao, K. V. Maintenance of sex-related genes and the co-occurrence of both mating types in Verticillium dahliae. PLoS ONE 9, e112145 (2014). · DOI
  84. Ni, M. et al. Unisexual and heterosexual meiotic reproduction generate aneuploidy and phenotypic diversity de novo in the yeast Cryptococcus neoformans. PLoS Biol. 11, e1001653 (2013). · DOI
  85. Couch, B. C. et al. Origins of host-specific populations of the blast pathogen Magnaporthe oryzae in crop domestication with subsequent expansion of pandemic clones on rice and weeds of rice. Genetics 170, 613–630 (2005). · DOI
  86. Jin, Y., Szarbo, L. J. & Carson, M. Century-old mystery of Puccinia striiformis life history solved with the identification of Berberis as an alternate host. Phytopathology 100, 432–435 (2010). · DOI
  87. Xhaard, C. et al. The genetic structure of the plant pathogenic fungus Melampsora larici-populina on its wild host is extensively impacted by host domestication. Mol. Ecol. 20, 2739–2755 (2011). · DOI
  88. Ali, S. et al. Origin, migration routes and worldwide population genetic structure of the wheat yellow rust pathogen Puccinia striiformis f.sp. tritici. PLoS Pathog. 10, e1003903 (2014). · DOI
  89. Saleh, D. et al. Sex at the origin: an Asian population of the rice blast fungus Magnaporthe oryzae reproduces sexually. Mol. Ecol. 21, 1330–1344 (2012). · DOI
  90. Ali, S., Leconte, M., Walker, A. S., Enjalbert, J. & Vallavieille-Pope, C. Reduction in the sex ability of worldwide clonal populations of Puccinia striiformis f.sp tritici. Fungal Genet. Biol. 47, 828–838 (2010). · DOI
  91. Smith, K. M. et al. Epigenetics of filamentous fungi. Rev. Cell Biol. Mol. Med. http://dx.doi.org/10.1002/3527600906.mcb.201100035 (2012). · DOI
  92. Dhillon, B., Cavaletto, J. R., Wood, K. V. & Goodwin, S. B. Accidental amplification and inactivation of a methyltransferase gene eliminates cytosine methylation in Mycosphaerella grami nicola. Genetics 186, 67–77 (2010). · DOI
  93. Levin, H. L. & Moran, J. V. Dynamic interactions between transposable elements and their hosts. Nat. Rev. Genet. 12, 615–627 (2011). · DOI · Paper page
  94. Daboussi, M.-J. & Capy, P. Transposable elements in filamentous fungi. Annu. Rev. Microbiol. 57, 275–299 (2003). · DOI
  95. Capy, P., Gasperi, G., Biémont, C. & Bazin, C. Stress and transposable elements: co-evolution or useful parasites? Heredity (Edinb.) 85, 101–106 (2000). · DOI · Paper page
  96. Dolgin, E. S. & Charlesworth, B. The fate of transposable elements in asexual populations. Genetics 174, 817–827 (2006). · DOI
  97. Halkett, F. et al. Genetic discontinuities and disequilibria in recently established populations of the plant pathogenic fungus Mycosphaerella fijiensis. Mol. Ecol. 19, 3909–3923 (2010). · DOI
  98. Munkacsi, A. B., Stoxen, S. & May, G. Ustilago maydis populations tracked maize through domestication and cultivation in the Americas. Proc. R. Soc. B Biol. Sci. 275, 1037–1046 (2008). · DOI
  99. Whittle, C. A. & Johannesson, H. Evidence of the accumulation of allele-specific non-synonymous substitutions in the young region of recombination suppression within the mating-type chromosomes of Neurospora tetrasperma. Heredity (Edinb.) 107, 305–314 (2011). · DOI
  100. Badouin, H. et al. Chaos of rearrangements in the mating-type chromosomes of the anther-smut fungus Microbotryum lychnidis-dioicae. Genetics 200, 1275–1284 (2015). · DOI
  101. Perlin, M. H. et al. Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus. BMC Genomics 16, 1 (2015). · DOI
  102. Okasha, S. Evolution and the Levels of Selection. (Oxford Univ. Press, 2006). · DOI
  103. Anderson, J. B. & Kohn, L. M. in Sex in Fungi: Molecular Determination and Evolutionary Implications. (eds Heitman J. et al.)333–348 (ASM Press, 2007).
  104. James, T. Y., Stenlid, J., Olson, Å. & Johannesson, H. Evolutionary significance of imbalanced nuclear ratios within heterokaryons of the Basidiomycete fungus Heterobasidion parviporum. Evolution. 62, 2279–2296 (2008). · DOI
  105. Olson, A. & Stenlid, J. Plant pathogens: mitochondrial control of fungal hybrid virulence. Nature 411, 438 (2001). · DOI
  106. Zheng, W. et al. High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus. Nat. Commun. 4, 2673 (2013). · DOI
  107. Stukenbrock, E. H. The role of hybridization in the evolution and emergence of new fungal plant pathogens. Phytopathology 106, 104–112 (2016). · DOI
  108. Stukenbrock, E. H., Christiansen, F. B., Hansen, T. T., Dutheil, J. Y. & Schierup, M. H. Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species. Proc. Natl Acad. Sci. USA 109, 10954–10959 (2012). · DOI
  109. Inderbitzin, P., Davis, R. M., Bostock, R. M. & Subbarao, K. V. The ascomycete Verticillium longisporum is a hybrid and a plant pathogen with an expanded host range. PLoS ONE 6, e18260 (2011). · DOI
  110. Shoji, J.-Y., Charlton, N. D., Yi, M., Young, C. A. & Craven, K. D. Vegetative hyphal fusion and subsequent nuclear behavior in Epichloë grass endophytes. PLoS ONE 10, e0121875 (2015). · DOI
  111. Schardl, C. & Craven, K. Interspecific hybridization in plant-associated fungi and oomycetes: a review. Mol. Ecol. 12, 2861–2873 (2003). · DOI
  112. Baack, E. J. & Rieseberg, L. H. A genomic view of introgression and hybrid speciation. Curr. Opin. Genet. Dev. 17, 513–518 (2007). · DOI · Paper page
  113. Richards, T. A. et al. Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi. Plant Cell 21, 1897–1911 (2009). · DOI
  114. Friesen, T. L. et al. Emergence of a new disease as a result of interspecific virulence gene transfer. Nat. Genet. 38, 953–956 (2006). · DOI
  115. Liu, Z. et al. The Tsn1–ToxA interaction in the wheat–Stagonospora nodorum pathosystem parallels that of the wheat–tan spot system. Genome 49, 1265–1273 (2006). · DOI
  116. Faris, J. D. et al. A unique wheat disease resistance-like gene governs effector-triggered susceptibility to necrotrophic pathogens. Proc. Natl Acad. Sci. USA 107, 13544–13549 (2010). · DOI
  117. Mcdonald, M. C., Ahren, D., Simpfendorfer, S., Milgate, A. & Solomon, P. S. The discovery of the virulence gene ToxA in the wheat and barley pathogen Bipolaris sorokiniana. Mol. Plant Pathol. http://dx.doi.org/10.1111/mpp.12535 (2017). This study shows that horizontal gene transfer of ToxA confers host-specific virulence across pathogens that infect wheat. · DOI
  118. Nikolaidis, N., Doran, N. & Cosgrove, D. J. Plant expansins in bacteria and fungi: evolution by horizontal gene transfer and independent domain fusion. Mol. Biol. Evol. 31, 376–386 (2014). · DOI
  119. de Jonge, R. et al. Tomato immune receptor Ve1 recognizes effector of multiple fungal pathogens uncovered by genome and RNA sequencing. Proc. Natl Acad. Sci. USA 109, 5110–5115 (2012). · DOI
  120. Gardiner, D. M. et al. Comparative pathogenomics reveals horizontally acquired novel virulence genes in fungi infecting cereal hosts. PLoS Pathog. 8, e1002952 (2012). · DOI
  121. Wright, S. & Finnegan, D. Genome evolution: sex and the transposable element. Curr. Biol. 11, R296–R299 (2001). · DOI
  122. Dang, Y., Yang, Q., Xue, Z. & Liu, Y. RNA interference in fungi: pathways, functions, and applications. Eukaryot. Cell 10, 1148–1155 (2011). · DOI
  123. Cambareri, E. B., Jensen, B. C., Schabtach, E. & Selker, E. U. Repeat-induced G-C to A-T mutations in Neurospora. Science 244, 1571–1575 (1989). · DOI
  124. Gladyshev, E. & Kleckner, N. Direct recognition of homology between double helices of DNA in Neurospora crassa. Nat. Commun. 5, 3509 (2014). · DOI
  125. Laurie, J. D. et al. Genome comparison of barley and maize smut fungi reveals targeted loss of RNA silencing components and species-specific presence of transposable elements. Plant Cell 24, 1733–1745 (2012). This study details a genome comparison of three closely related smut fungi that reveals transposable element expansion in Ustilago hordei and the loss of RNAi components in U. maydis. · DOI
  126. Hood, M. E., Katawczik, M. & Giraud, T. Repeat-induced point mutation and the population structure of transposable elements in Microbotryum violaceum. Genetics 170, 1081–1089 (2005). · DOI
  127. Idnurm, A. & Howlett, B. J. Analysis of loss of pathogenicity mutants reveals that repeat-induced point mutations can occur in the Dothideomycete Leptosphaeria maculans. Fungal Genet. Biol. 39, 31–37 (2003). · DOI
  128. Zemach, A., McDaniel, I. E., Silva, P. & Zilberman, D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328, 916–919 (2010). · DOI
  129. Galagan, J. E. & Selker, E. U. RIP: The evolutionary cost of genome defense. Trends Genet. 20, 417–423 (2004). · DOI
  130. Studt, L. et al. Knock-down of the methyltransferase Kmt6 relieves H3K27me3 and results in induction of cryptic and otherwise silent secondary metabolite gene clusters in Fusarium fujikuroi. Environ. Microbiol. 18, 4037–4054 (2016). · DOI
  131. Connolly, L. R., Smith, K. M. & Freitag, M. The Fusarium graminearum histone H3 K27 methyltransferase KMT6 regulates development and expression of secondary metabolite gene clusters. PLoS Genet. 9, e1003916 (2013). · DOI · Paper page
  132. Letunic, I. & Bork, P. Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23, 127–128 (2007). · DOI · Paper page
  133. Grandaubert, J., Bhattacharyya, A. & Stukenbrock, E. H. RNA-seq based gene annotation and comparative genomics of four fungal grass pathogens in the genus Zymoseptoria identify novel orphan genes and species-specific invasions of transposable elements. G3 (Bethesda) 5, 1323–1333 (2015). · DOI
  134. Vanheule, A. et al. Living apart together: crosstalk between the core and supernumerary genomes in a fungal plant pathogen. BMC Genomics 17, 670 (2016). · DOI
  135. Spanu, P. D. et al. Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism. Science 330, 1543–1546 (2010). · DOI · Paper page
  136. Wicker, T. et al. The wheat powdery mildew genome shows the unique evolution of an obligate biotroph. Nat. Genet. 45, 1092–1096 (2013). · DOI
  137. Hacquard, S. et al. Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts. Proc. Natl Acad. Sci. USA 110, E2219–E2228 (2013). · DOI
  138. Dean, R. A. et al. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 434, 980–986 (2005). · DOI
  139. Forgetta, V. et al. Sequencing of the Dutch elm disease fungus genome using the Roche/454 GS-FLX Titanium System in a comparison of multiple genomics core facilities. J. Biomol. Tech. 24, 39–49 (2013).
  140. Cuomo, C. A. et al. The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization. Science 317, 1400–1402 (2007). · DOI

Cited by

Metadata

Authors
Möller, M., & Stukenbrock, E. H.
Venue
Nature Reviews Microbiology
Publisher
Springer Science and Business Media LLC
Published
2017-08-07
Volume
15
Issue
12
Pages
756-771
ISSN
  • 1740-1526 (ISSN-L)
  • 1740-1534
DOI
10.1038/nrmicro.2017.76
OpenAlex
W2742822384
Cited by
432
References
5
FWCI
3.51
Type
journal article
Language
en
Update notices
erratum (2017-12-01)
Open access
closed
Licence

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Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.