1932

Abstract

Strategies to manage plant disease—from use of resistant varieties to crop rotation, elimination of reservoirs, landscape planning, surveillance, quarantine, risk modeling, and anticipation of disease emergences—all rely on knowledge of pathogen host range. However, awareness of the multitude of factors that influence the outcome of plant–microorganism interactions, the spatial and temporal dynamics of these factors, and the diversity of any given pathogen makes it increasingly challenging to define simple, all-purpose rules to circumscribe the host range of a pathogen. For bacteria, fungi, oomycetes, and viruses, we illustrate that host range is often an overlapping continuum—more so than the separation of discrete pathotypes—and that host jumps are common. By setting the mechanisms of plant–pathogen interactions into the scales of contemporary land use and Earth history, we propose a framework to assess the frontiers of host range for practical applications and research on pathogen evolution.

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2019-08-25
2024-04-19
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Literature Cited

  1. 1. 
    Andika IB, Wei S, Cao C, Salaipeth L, Kondo H, Sun L 2017. Phytopathogenic fungus hosts a plant virus: a naturally occurring cross-kingdom viral infection. PNAS 114:12267–72
    [Google Scholar]
  2. 2. 
    Arias T, Beilstein MA, Tang M, McKain MR, Pires JC 2014. Diversification times among Brassica (Brassicaceae) crops suggest hybrid formation after 20 million years of divergence. Am. J. Bot. 101:86–91
    [Google Scholar]
  3. 3. 
    Armijos Jaramillo VD, Vargas WA, Sukno SA, Thon MR 2013. Horizontal transfer of a subtilisin gene from plants into an ancestor of the plant pathogenic fungal genus Colletotrichum. PLOS ONE 8:3e59078
    [Google Scholar]
  4. 4. 
    Arriel DAA, Fonseca NR, Guimarães LMS, Hermenegildo PS, Ma RG, Júnior NB 2014. Wilt and die-back of Eucalyptus spp. caused by Erwinia psidii in Brazil. For. Pathol. 44:255–65
    [Google Scholar]
  5. 5. 
    Bahri B, Kaltz O, Leconte M, De Vallavieille-Pope C, Enjalbert J 2009. Tracking costs of virulence in natural populations of the wheat pathogen, Puccinia striiformis f.sp. tritici. BMC Evol. Biol. 9:26
    [Google Scholar]
  6. 6. 
    Bahri BA. 2008. Adaptation et structuration spatiale des populations méditerranéennes de rouille jaune du blé (Puccinia striiformis f.sp. tritici). PhD Thesis, Univ. Paris Sud Orsay:Fr. 250
    [Google Scholar]
  7. 7. 
    Baldi P, La Porta N 2017. Xylella fastidiosa: host range and advance in molecular identification techniques. Front. Plant Sci. 8:944
    [Google Scholar]
  8. 8. 
    Barba-Montoya J, dos Reis M, Schneider H, Donoghue PCJ, Yang Z 2018. Constraining uncertainty in the timescale of angiosperm evolution and the veracity of a Cretaceous Terrestrial Revolution. New Phytol 218:819–34
    [Google Scholar]
  9. 9. 
    Barrett LG, Encinas-Viso F, Burdon JJ, Thrall PH 2015. Specialization for resistance in wild host-pathogen interaction networks. Front. Plant Sci. 6:761
    [Google Scholar]
  10. 10. 
    Barrett LG, Heil M. 2012. Unifying concepts and mechanisms in the specificity of plant-enemy interactions. Trends Plant Sci 17:5282–92
    [Google Scholar]
  11. 11. 
    Barrett LG, Kniskern JM, Bodenhausen N, Zhang W, Bergelson J 2009. Continua of specificity and virulence in plant host-pathogen interactions: causes and consequences. New Phytol 183:513–29
    [Google Scholar]
  12. 12. 
    Battistuzzi FU, Feijao A, Hedges SB 2004. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol. Biol. 4:44
    [Google Scholar]
  13. 13. 
    Baumler DJ, Ma B, Reed JL, Perna NT 2013. Inferring ancient metabolism using ancestral core metabolic models of enterobacteria. BMC Syst. Biol. 7:46
    [Google Scholar]
  14. 14. 
    Belhaj K, Cano LM, Prince DC, Kemen A, Yoshida K et al. 2017. Arabidopsis late blight: infection of a nonhost plant by Albugo laibachii enables full colonization by Phytophthora infestans. Cell. Microbiol 19:1e12628
    [Google Scholar]
  15. 15. 
    Benevenuto J, Teixeira-Silva NS, Kuramae EE, Croll D, Monteiro-Vitorello CB 2018. Comparative genomics of smut pathogens: insights from orphans and positively selected genes into host specialization. Front. Microbiol. 9:660
    [Google Scholar]
  16. 16. 
    Bera S, Moreno-Pérez MG, García-Figuera S, Pagán I, Fraile A et al. 2017. Pleiotropic effects of resistance-breaking mutations on particle stability provide insight into life history evolution of a plant RNA virus. J. Virol. 91:18e00435–17
    [Google Scholar]
  17. 17. 
    Berbee ML, James TY, Strullu-Derrien C 2017. Early diverging fungi: diversity and impact at the dawn of terrestrial life. Annu. Rev. Microbiol. 71:41–60
    [Google Scholar]
  18. 18. 
    Berge O, Monteil CL, Bartoli C, Chandeysson C, Guilbaud C et al. 2014. A user's guide to a data base of the diversity of Pseudomonas syringae and its application to classifying strains in this phylogenetic complex. PLOS ONE 9:9e105547
    [Google Scholar]
  19. 19. 
    Bergelson J, Dwyer G, Emerson JJ 2001. Models and data on plant-enemy coevolution. Annu. Rev. Genet. 35:469–99
    [Google Scholar]
  20. 20. 
    Bergelson J, Purrington CB. 1996. Surveying patterns in the cost of resistance in plants. Am. Nat. 148:536–58
    [Google Scholar]
  21. 21. 
    Bignell DRD, Fyans JK, Cheng Z 2014. Phytotoxins produced by plant pathogenic Streptomyces species. J. Appl. Microbiol. 116:223–35
    [Google Scholar]
  22. 22. 
    Blanco LP, Payne BL, Feyertag F, Alvarez-Ponce D 2018. Proteins of generalist and specialist pathogens differ in their amino acid composition. Life Sci. Alliance 1:4e201800017
    [Google Scholar]
  23. 23. 
    Bonfante P, Genre A. 2015. Arbuscular mycorrhizal dialogues: Do you speak “plantish” or “fungish”?. Trends Plant Sci 20:150–54
    [Google Scholar]
  24. 24. 
    Brady CL, Cleenwerck I, van der Westhuizen L, Venter SN, Coutinho T, De Vos P 2012. Pantoea rodasii sp. nov., Pantoea rwandensis sp. nov. and Pantoea wallisii sp. nov., isolated from Eucalyptus. Int. J. Syst. Evol. Microbiol 62:1457–64
    [Google Scholar]
  25. 25. 
    Brown JKM. 2003. A cost of disease resistance: paradigm or peculiarity?. Trends Genet 19:667–71
    [Google Scholar]
  26. 26. 
    Brundrett MC. 2002. Coevolution of roots and mycorrhizas of land plants. New Phytol 154:275–304
    [Google Scholar]
  27. 27. 
    Chappell TM, Rausher MD. 2016. Evolution of host range in Coleosporium ipomoeae, a plant pathogen with multiple hosts. PNAS 113:5346–51
    [Google Scholar]
  28. 28. 
    Charon J, Barra A, Walter J, Millot P, Hébrard E et al. 2018. First experimental assessment of protein intrinsic disorder involvement in an RNA virus natural adaptive process. Mol. Biol. Evol. 35:38–49
    [Google Scholar]
  29. 29. 
    Chater KF, Biró S, Lee KJ, Palmer T, Schrempf H 2010. The complex extracellular biology of Streptomyces. FEMS Microbiol. Rev 34:171–98
    [Google Scholar]
  30. 30. 
    Chatterjee S, Almeida RPP, Lindow SE 2008. Living in two worlds: the plant and insect lifestyles of Xylella fastidiosa. Annu. Rev. Phytopathol 46:243–71
    [Google Scholar]
  31. 31. 
    Chaverri P, Samuels GJ. 2013. Evolution of habitat preference and nutrition mode in a cosmopolitan fungal genus with evidence of interkingdom host jumps and major shifts in ecology. Evolution 67:2823–37
    [Google Scholar]
  32. 32. 
    Chen K-C, Chiang C-H, Raja JAJ, Liu F-L, Tai C-H, Yeh S-D 2008. A single amino acid of NIaPro of Papaya ringspot virus determines host specificity for infection of papaya. Mol. Plant-Microbe Interact. 21:1046–57
    [Google Scholar]
  33. 33. 
    Choi YJ, Thines M. 2015. Host jumps and radiation, not co-divergence drives diversification of obligate pathogens. A case study in downy mildews and Asteraceae. PLOS ONE 10:7e0133655
    [Google Scholar]
  34. 34. 
    Coletta-Filho HD, Francisco CS, Lopes JRS, Muller C, Almeida RPP 2017. Homologous recombination and Xylella fastidiosa host-pathogen associations in South America. Phytopathology 107:305–12
    [Google Scholar]
  35. 35. 
    Consonni C, Humphry ME, Hartmann HA, Livaja M, Durner J et al. 2006. Conserved requirement for a plant host cell protein in powdery mildew pathogenesis. Nat. Genet. 38:716–20
    [Google Scholar]
  36. 36. 
    Cornman RS. 2017. Available genetic data do not support adaptation of Tobacco ringspot virus to an arthropod host. mBio 8:1e01875–16
    [Google Scholar]
  37. 37. 
    Curtis MD, Gore J, Oliver RP 1994. The phylogeny of the tomato leaf mould fungus Cladosporium fulvum syn. Fulvia fulva by analysis of rDNA sequences. Curr. Genet. 25:318–22
    [Google Scholar]
  38. 38. 
    Cuthill JH, Charleston MA. 2013. A simple model explains the dynamics of preferential host switching among mammal RNA viruses. Evolution 67:980–90
    [Google Scholar]
  39. 39. 
    Dasgupta R, Garcia BH, Goodman RM 2001. Systemic spread of an RNA insect virus in plants expressing plant viral movement protein genes. PNAS 98:4910–15
    [Google Scholar]
  40. 40. 
    Daverdin G, Rouxel T, Gout L, Aubertot J-N, Fudal I et al. 2012. Genome structure and reproductive behaviour influence the evolutionary potential of a fungal phytopathogen. PLOS Pathog 8:11e1003020
    [Google Scholar]
  41. 41. 
    Delbianco A, Czwienczek E, Pautasso M, Kozelska S, Monguidi M, Stancanelli G 2019. A new resource for research and risk analysis: the updated European Food Safety Authority database of Xylella spp. host plant species. Phytopathology 109:2213–15
    [Google Scholar]
  42. 42. 
    Depotter JRL, Seidl MF, Wood TA, Thomma BPHJ 2016. Interspecific hybridization impacts host range and pathogenicity of filamentous microbes. Curr. Opin. Microbiol. 32:7–13
    [Google Scholar]
  43. 43. 
    de Vienne DM, Giraud T, Shykoff JA 2007. When can host shifts produce congruent host and parasite phylogenies? A simulation approach. J. Evol. Biol. 20:1428–38
    [Google Scholar]
  44. 44. 
    de Vienne DM, Refrégier G, López-Villavicencio M, Tellier A, Hood ME, Giraud T 2013. Cospeciation versus host-shift speciation: methods for testing, evidence from natural associations and relation to coevolution. New Phytol 198:347–85
    [Google Scholar]
  45. 45. 
    Diop SI, Geering ADW, Alfama-Depauw F, Loaec M, Teycheney PY, Maumus F 2018. Tracheophyte genomes keep track of the deep evolution of the Caulimoviridae. Sci. Rep 8:572
    [Google Scholar]
  46. 46. 
    Dong S, Stam R, Cano LM, Song J, Sklenar J et al. 2014. Effector specialization in a lineage of the Irish potato famine pathogen. Science 343:552–55
    [Google Scholar]
  47. 47. 
    Dordas C. 2008. Role of nutrients in controlling plant diseases in sustainable agriculture. A review. Agron. Sustain. Dev. 28:33–46
    [Google Scholar]
  48. 48. 
    Du J, Tian Z, Hans CS, Laten HM, Cannon SB et al. 2010. Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison. Plant J 63:584–98
    [Google Scholar]
  49. 49. 
    Ellis J. 2006. Insights into nonhost disease resistance: Can they assist disease control in agriculture?. Plant Cell 18:523–28
    [Google Scholar]
  50. 50. 
    Escudero M. 2015. Phylogenetic congruence of parasitic smut fungi (Anthracoidea, Anthracoideaceae) and their host plants (Carex, Cyperaceae): cospeciation or host-shift speciation?. Am. J. Bot. 102:1108–14
    [Google Scholar]
  51. 51. 
    Farrell BD, Sequeira AS, Meara BCO, Normark BB, Chung JH, Jordal BH 2001. The evolution of agriculture in beetles (Curculionidae: Scolytinae and Platypodinae). Evolution 55:102011–27
    [Google Scholar]
  52. 52. 
    Fenton A, Antonovics J, Brockhurst MA 2009. Inverse‐gene‐for‐gene infection genetics and coevolutionary dynamics. Am. Nat. 174:E230–42
    [Google Scholar]
  53. 53. 
    Fischer E, Dumbo B, Dehling M, Killmann D 2011. Biodiversity inventory for key wetlands in Rwanda Rep., Cent. d'Echange CHM Rwanda Kigali: http://rw.chm-cbd.net/implementation/rapport-et-documents-nationaux/biodiversity-inventory-key-wetlands-rwanda-final-report
  54. 54. 
    Flor HH. 1956. The complementary genic systems in flax and flax rust. Adv. Genet. 8:29–54
    [Google Scholar]
  55. 55. 
    Flores CO, Meyer JR, Valverde S, Farr L, Weitz JS 2011. Statistical structure of host-phage interactions. PNAS 108:E288–97
    [Google Scholar]
  56. 56. 
    Fonseca JP, Mysore KS. 2019. Genes involved in nonhost disease resistance as a key to engineer durable resistance in crops. Plant Sci 279:108–16
    [Google Scholar]
  57. 57. 
    Fournet S, Eoche-Bosy D, Renault L, Hamelin FM, Montarry J 2016. Adaptation to resistant hosts increases fitness on susceptible hosts in the plant parasitic nematode Globodera pallida. . Ecol. Evol 6:2559–68
    [Google Scholar]
  58. 58. 
    Fraile A, Hily J, Pagán I, Pacios LF, García-Arenal F 2014. Host resistance selects for traits unrelated to resistance-breaking that affect fitness in a plant virus. Mol. Biol. Evol. 31:928–39
    [Google Scholar]
  59. 59. 
    García-Arenal F, Fraile A. 2013. Trade-offs in host range evolution of plant viruses. Plant Pathol 62:2–9
    [Google Scholar]
  60. 60. 
    García-Arenal F, McDonald BA. 2003. An analysis of the durability of resistance to plant viruses. Phytopathology 93:8941–52
    [Google Scholar]
  61. 61. 
    Gibbs AJ, Fargette D, García-Arenal F, Gibbs MJ 2010. Time: the emerging dimension of plant virus studies. J. Gen. Virol. 91:13–22
    [Google Scholar]
  62. 62. 
    Gilbert GS, Magarey R, Suiter K, Webb CO 2012. Evolutionary tools for phytosanitary risk analysis: phylogenetic signal as a predictor of host range of plant pests and pathogens. Evol. Appl. 5:869–78
    [Google Scholar]
  63. 63. 
    Gilbert GS, Parker IM. 2016. The evolutionary ecology of plant disease: a phylogenetic perspective. Annu. Rev. Phytopathol. 54:549–78
    [Google Scholar]
  64. 64. 
    Glaeser SP, Imani J, Alabid I, Guo H, Kumar N et al. 2016. Non-pathogenic Rhizobium radiobacter F4 deploys plant beneficial activity independent of its host Piriformospora indica. ISME J 10:871–84
    [Google Scholar]
  65. 65. 
    Göker M, Scheuner C, Klenk H-P, Stielow JB, Menzel W 2011. Codivergence of mycoviruses with their hosts. PLOS ONE 6:7e22252
    [Google Scholar]
  66. 66. 
    González AM, Marcel TC, Niks RE 2012. Evidence for a minor gene-for-minor gene interaction explaining nonhypersensitive polygenic partial disease resistance. Phytopathology 102:1086–93
    [Google Scholar]
  67. 67. 
    Grattapaglia D, Vaillancourt RE, Shepherd M, Thumma BR, Foley W et al. 2012. Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus. Tree Genet. Genomes 8:463–508
    [Google Scholar]
  68. 68. 
    Grosberg RK, Hart MW. 2000. Mate selection and the evolution of highly polymorphic self/nonself recognition genes. Science 289:2111–14
    [Google Scholar]
  69. 69. 
    Grünwald NJ, Goss EM, Press CM 2008. Phytophthora ramorum: a pathogen with a remarkably wide host range causing sudden oak death on oaks and ramorum blight on woody ornamentals. Mol. Plant Pathol. 9:729–40
    [Google Scholar]
  70. 70. 
    Haas W, Haberl B, Kalbe M, Kömer M 1995. Snail-host-finding by Miracidia and Cercariae: chemical host cues. Parasitol. Today 11:468–72
    [Google Scholar]
  71. 71. 
    Hacquard S, Kracher B, Hiruma K, Münch PC, Garrido-Oter R et al. 2016. Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi. Nat. Commun. 7:11362
    [Google Scholar]
  72. 72. 
    Hall AR, Scanlan PD, Buckling A 2011. Bacteria‐phage coevolution and the emergence of generalist pathogens. Am. Nat. 177:44–53
    [Google Scholar]
  73. 73. 
    Hedges SB, Marin J, Suleski M, Paymer M, Kumar S 2015. Tree of life reveals clock-like speciation and diversification. Mol. Biol. Evol. 32:835–45
    [Google Scholar]
  74. 74. 
    Hess J, Skrede I, Chaib De Mares M, Hainaut M, Henrissat B, Pringle A 2018. Rapid divergence of genome architectures following the origin of an ectomycorrhizal symbiosis in the genus Amanita. Mol. Biol. Evol 35:2786–804
    [Google Scholar]
  75. 75. 
    Hillung J, Cuevas JM, Valverde S, Elena SF 2014. Experimental evolution of an emerging plant virus in host genotypes that differ in their susceptibility to infection. Evolution 68:92467–80
    [Google Scholar]
  76. 76. 
    Hjulsager CK, Olsen BS, Jensen DMK, Cordea MI, Krath BN et al. 2006. Multiple determinants in the coding region of Pea seed-borne mosaic virus P3 are involved in virulence against sbm-2 resistance. Virology 355:52–61
    [Google Scholar]
  77. 77. 
    Horn M, Collingro A, Schmitz-Esser S, Beier CL, Purkhold U et al. 2004. Illuminating the evolutionary history of Chlamydiae. Science 304:5671728–30
    [Google Scholar]
  78. 78. 
    Hou S, Jamieson P, He P 2018. The cloak, dagger, and shield: proteases in plant-pathogen interactions. Biochem. J. 475:2491–509
    [Google Scholar]
  79. 79. 
    Huang HC, Hsieh TF, Erickson RS 2003. Biology and epidemiology of Erwinia rhapontici, causal agent of pink seed and crown rot of plants. Plant Pathol. Bull. 12:69–76
    [Google Scholar]
  80. 80. 
    Inoue Y, Vy TTP, Yoshida K, Asano H, Mitsuoka C et al. 2017. Evolution of the wheat blast fungus through functional losses in a host specificity determinant. Science 357:634680–83
    [Google Scholar]
  81. 81. 
    Jackson A. 2004. A reconciliation analysis of host switching in plant-fungal symbioses. Evolution 58:1909–23
    [Google Scholar]
  82. 82. 
    Jeong S, Ritchie N, Myrold D 1999. Molecular phylogenies of plants and Frankia support multiple origins of actinorhizal symbioses. Mol. Phylogenet. Evol. 13:493–503
    [Google Scholar]
  83. 83. 
    Kabbage M, Yarden O, Dickman MB 2015. Pathogenic attributes of Sclerotinia sclerotiorum: Switching from a biotrophic to necrotrophic lifestyle. Plant Sci 233:53–60
    [Google Scholar]
  84. 84. 
    Kachroo A, Vincelli P, Kachroo P 2017. Signaling mechanisms underlying resistance responses: What have we learned, and how is it being applied?. Phytopathology 107:1452–61
    [Google Scholar]
  85. 85. 
    Karasov TL, Almario J, Friedemann C, Ding W, Giolai M et al. 2018. Arabidopsis thaliana and Pseudomonas pathogens exhibit stable associations over evolutionary timescales. Cell Host Microbe 24:168–79
    [Google Scholar]
  86. 86. 
    Karasov TL, Kniskern JM, Gao L, DeYoung BJ, Ding J et al. 2014. The long-term maintenance of a resistance polymorphism through diffuse interactions. Nature 512:436–40
    [Google Scholar]
  87. 87. 
    Kidner J, Moritz RAF. 2013. The Red Queen process does not select for high recombination rates in haplodiploid hosts. Evol. Biol. 40:377–84
    [Google Scholar]
  88. 88. 
    King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ 2012. Virus Taxonomy: Classification and Nomenclature of Viruses: Ninth Report of the International Committee on Taxonomy of Viruses San Diego, CA: Elsevier Acad1,327 pp.
  89. 89. 
    Kourelis J, van der Hoorn RAL 2018. Defended to the nines: 25 years of resistance gene cloning identifies nine mechanisms for R protein function. Plant Cell 30:285–99
    [Google Scholar]
  90. 90. 
    Lebreton F, Manson AL, Saavedra JT, Straub TJ, Earl AM, Gilmore MS 2017. Tracing the enterococci from Paleozoic origins to the hospital. Cell 169:849–61
    [Google Scholar]
  91. 91. 
    Lefeuvre P, Harkins GW, Lett JM, Briddon RW, Chase MW et al. 2011. Evolutionary time-scale of the begomoviruses: evidence from integrated sequences in the Nicotiana genome. PLOS ONE 6:5e19193
    [Google Scholar]
  92. 92. 
    Lenski RE, Levin BR. 1985. Constraints on the coevolution of bacteria and virulent phage: a model, some experiments, and predictions for natural communities. Am. Nat. 125:585–602
    [Google Scholar]
  93. 93. 
    Li JL, Cornman RS, Evans JD, Pettis J, Zhao Y et al. 2014. Systemic spread and propagation of a plant-pathogenic virus in European honeybees. Apis mellifera. mBio 5:e00898–13
    [Google Scholar]
  94. 94. 
    Li P, Day B. 2019. Battlefield cytoskeleton: turning the tide on plant immunity. Mol. Plant-Microbe Interact. 32:25–34
    [Google Scholar]
  95. 95. 
    Liang Y, Tóth K, Cao Y, Tanaka K, Espinoza C, Stacey G 2014. Lipochitooligosaccharide recognition: an ancient story. New Phytol 204:289–96
    [Google Scholar]
  96. 96. 
    Lofgren LA, LeBlanc NR, Certano AK, Nachtigall J, LaBine KM et al. 2018. Fusarium graminearum: pathogen or endophyte of North American grasses?. New Phytol 217:1203–12
    [Google Scholar]
  97. 97. 
    Loria R, Coombs J, Yoshida M, Kers J, Bukhalid R 2003. A paucity of bacterial root diseases: Streptomyces succeeds where others fail. Physiol. Mol. Plant Pathol. 62:65–72
    [Google Scholar]
  98. 98. 
    Lowe-Power TM, Khokhani D, Allen C 2018. How Ralstonia solanacearum exploits and thrives in the flowing plant xylem environment. Trends Microbiol 26:929–42
    [Google Scholar]
  99. 99. 
    Luo M, Sheng Q, Wang CL, Zhang XL 2018. First report of fruit spot on pepper caused by Erwinia aphidicola in China. Plant Dis 102:1445
    [Google Scholar]
  100. 100. 
    Marin J, Battistuzzi FU, Brown AC, Hedges SB 2017. The timetree of prokaryotes: new insights into their evolution and speciation. Mol. Biol. Evol. 34:437–46
    [Google Scholar]
  101. 101. 
    Martin F, Kohler A, Murat C, Veneault-Fourrey C, Hibbett DS 2016. Unearthing the roots of ectomycorrhizal symbioses. Nat. Rev. Microbiol. 14:760–73
    [Google Scholar]
  102. 102. 
    Martinetti D, Soubeyrand S. 2019. Identifying lookouts for epidemio-surveillance: application to the emergence of Xylella fastidiosa in France. Phytopathology 109:265–76
    [Google Scholar]
  103. 103. 
    Matari NH, Blair JE. 2014. A multilocus timescale for oomycete evolution estimated under three distinct molecular clock models. BMC Evol. Biol. 14:101
    [Google Scholar]
  104. 104. 
    McDonald BA, Linde C. 2002. Pathogen population genetics, evolutionary potential, and durable resistance. Annu. Rev. Phytopathol. 40:349–79
    [Google Scholar]
  105. 105. 
    McTaggart AR, Shivas RG, Nest MA, Roux J, Wingfield BD, Wingfield MJ 2015. Host jumps shaped the diversity of extant rust fungi (Pucciniales). New Phytol 209:1149–58
    [Google Scholar]
  106. 106. 
    Menardo F, Praz CR, Wyder S, Ben-David R, Bourras S et al. 2016. Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species. Nat. Genet. 48:201–5
    [Google Scholar]
  107. 107. 
    Méthot P-O, Alizon S. 2014. What is a pathogen? Toward a process view of host-parasite interactions. Virulence 5:775–85
    [Google Scholar]
  108. 108. 
    Morris CE, Lamichhane JR, Nikolić I, Stanković S, Moury B 2019. The overlapping continuum of host range among strains in the Pseudomonas syringae complex. BMC Phytopathol. Res. 1:4
    [Google Scholar]
  109. 109. 
    Moury B, Fabre F, Hébrard E, Froissart R 2017. Determinants of host species range in plant viruses. J. Gen. Virol. 98:862–73
    [Google Scholar]
  110. 110. 
    Moury B, Janzac B, Ruellan Y, Simon V, Ben Khalifa M et al. 2014. Interaction patterns between Potato virus Y and eIF4E-mediated recessive resistance in the Solanaceae. J. Virol. 88:9799–807
    [Google Scholar]
  111. 111. 
    Munkacsi AB, Stoxen S, May G 2007. Domestication of maize, sorghum, and sugarcane did not drive the divergence of their smut pathogens. Evolution 61:388–403
    [Google Scholar]
  112. 112. 
    Mysore KS, Ryu C-M. 2004. Nonhost resistance: How much do we know?. Trends Plant Sci 9:97–104
    [Google Scholar]
  113. 113. 
    Navaud O, Barbacci A, Taylor A, Clarkson JP, Raffaele S 2018. Shifts in diversification rates and host jump frequencies shaped the diversity of host range among Sclerotiniaceae fungal plant pathogens. Mol. Ecol. 27:1309–23
    [Google Scholar]
  114. 114. 
    Neuhauser S, Kirchmair M, Bulman S, Bass D 2014. Cross-kingdom host shifts of phytomyxid parasites. BMC Evol. Biol. 14:133
    [Google Scholar]
  115. 115. 
    Nunney L, Vickerman DB, Bromley RE, Russell SA, Hartman JR et al. 2013. Recent evolutionary radiation and host plant specialization in the Xylella fastidiosa subspecies native to the United States. Appl. Environ. Microbiol. 79:2189–200
    [Google Scholar]
  116. 116. 
    O'Brien HE, Thakur S, Gong Y, Fung P, Zhang J et al. 2012. Extensive remodeling of the Pseudomonas syringae pv. avellanae type III secretome associated with two independent host shifts onto hazelnut. BMC Microbiol 12:141
    [Google Scholar]
  117. 117. 
    Oliver JE, Whitfield AE. 2016. The genus Tospovirus: emerging bunyaviruses that threaten food security. Annu. Rev. Virol. 3:101–24
    [Google Scholar]
  118. 118. 
    Oliver R, Ipcho S. 2004. Arabidopsis pathology breathes new life into the necrotrophs-versus-biotrophs classification of fungal pathogens. Mol. Plant Pathol. 6:160–69
    [Google Scholar]
  119. 119. 
    Pagán I, Firth C, Holmes EC 2010. Phylogenetic analysis reveals rapid evolutionary dynamics in the plant RNA virus genus Tobamovirus. J. Mol. Evol. 71:298–307
    [Google Scholar]
  120. 120. 
    Pancher M, Antonielli L, Campisano A, Ometto L, Yousaf S et al. 2014. Interkingdom transfer of the acne-causing agent, Propionibacterium acnes, from human to grapevine. Mol. Biol. Evol. 31:1059–65
    [Google Scholar]
  121. 121. 
    Parker IM, Gilbert GS. 2004. The evolutionary ecology of novel plant-pathogen interactions. Annu. Rev. Ecol. Evol. Syst. 35:675–700
    [Google Scholar]
  122. 122. 
    Peterson KR, Pfister DH, Bell CD 2010. Cophylogeny and biogeography of the fungal parasite Cyttaria and its host Nothofagus, southern beech. Mycologia 102:1417–25
    [Google Scholar]
  123. 123. 
    Petrzik K, Vondrák J, Barták M, Peksa O, Kubešová O 2014. Lichens: a new source or yet unknown host of herbaceous plant viruses?. Eur. J. Plant Pathol. 138:549–59
    [Google Scholar]
  124. 124. 
    Poulicard N, Pinel-Galzi A, Traoré O, Vignols F, Ghesquière A et al. 2012. Historical contingencies modulate the adaptability of Rice yellow mottle virus. PLOS Pathog 8:1e1002482
    [Google Scholar]
  125. 125. 
    Ranf S. 2018. Pattern recognition receptors: versatile genetic tools for engineering broad-spectrum disease resistance in crops. Agronomy 8:8134
    [Google Scholar]
  126. 126. 
    Redak RA, Purcell AH, Lopes JRS, Blua MJ, Mizell RF III, Andersen PC 2004. The biology of xylem fluid-feeding insect vectors of Xylella fastidiosa and their relation to disease epidemiology. Annu. Rev. Entomol. 49:243–70
    [Google Scholar]
  127. 127. 
    Refrégier G, Le Gac M, Jabbour F, Widmer A, Shykoff JA et al. 2008. Cophylogeny of the anther smut fungi and their caryophyllaceous hosts: prevalence of host shifts and importance of delimiting parasite species for inferring cospeciation. BMC Evol. Biol. 8:100
    [Google Scholar]
  128. 128. 
    Rolff J, Siva-Jothy MT. 2003. Invertebrate ecological immunology. Science 301:472–75
    [Google Scholar]
  129. 129. 
    Roossinck MJ. 2017. Deep sequencing for discovery and evolutionary analysis of plant viruses. Virus Res 239:82–86
    [Google Scholar]
  130. 130. 
    Roossinck MJ. 2018. Evolutionary and ecological links between plant and fungal viruses. New Phytol 221:86–92
    [Google Scholar]
  131. 131. 
    Rouxel T, Grandaubert J, Hane JK, Hoede C, Van De Wouw AP et al. 2011. Effector diversification within compartments of the Leptosphaeria maculans genome affected by repeat-induced point mutations. Nat. Commun. 2:202
    [Google Scholar]
  132. 132. 
    Roy BA. 2001. Patterns of association between crucifers and their flower-mimic pathogens: Host-jumps are more common than coevolution or cospeciation. Evolution 55:41–53
    [Google Scholar]
  133. 133. 
    Sacristán S, García-Arenal F. 2008. The evolution of virulence and pathogenicity in plant pathogen populations. Mol. Plant Pathol. 9:369–84
    [Google Scholar]
  134. 134. 
    Savory EA, Fuller SL, Weisberg AJ, Thomas WJ, Gordon MI et al. 2017. Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management. eLife 6:e30928
    [Google Scholar]
  135. 135. 
    Schardl CL, Craven KD, Speakman S, Stromberg A, Lindstrom A, Yoshida R 2008. A novel test for host-symbiont codivergence indicates ancient origin of fungal endophytes in grasses. Syst. Biol. 57:483–98
    [Google Scholar]
  136. 136. 
    Schulze-Lefert P, Panstruga R. 2011. A molecular evolutionary concept connecting nonhost resistance, pathogen host range, and pathogen speciation. Trends Plant Sci 16:117–25
    [Google Scholar]
  137. 137. 
    Sdzielewska Toro K, Brachmann A 2016. The effector candidate repertoire of the arbuscular mycorrhizal fungus Rhizophagus clarus. BMC Genom 17:101
    [Google Scholar]
  138. 138. 
    Selosse MA, Strullu-Derrien C, Martin FM, Kamoun S, Kenrick P 2015. Plants, fungi and oomycetes: a 400-million year affair that shapes the biosphere. New Phytol 206:501–6
    [Google Scholar]
  139. 139. 
    Sharma R, Mishra B, Runge F, Thines M 2014. Gene loss rather than gene gain is associated with a host jump from monocots to dicots in the smut fungus Melanopsichium pennsylvanicum.Genome Biol. Evol 6:82034–49
    [Google Scholar]
  140. 140. 
    Sprent JI, James EK. 2007. Legume evolution: Where do nodules and mycorrhizas fit. in? Plant Physiol 144:575–81
    [Google Scholar]
  141. 141. 
    Springer DJ, Mohan R, Heitman J 2017. Plants promote mating and dispersal of the human pathogenic fungus Cryptococcus. PLOS ONE 12:2e0171695
    [Google Scholar]
  142. 142. 
    Suehiro N, Natsuaki T, Watanabe T, Okuda S 2018. An important determinant of the ability of Turnip mosaic virus to infect Brassica spp. and/or Raphanus sativus is in its P3 protein. J. Gen. Virol. 85:2087–98
    [Google Scholar]
  143. 143. 
    Summerell BA, Laurence MH, Liew ECY, Leslie JF 2010. Biogeography and phylogeography of Fusarium: a review. Fungal Divers 44:3–13
    [Google Scholar]
  144. 144. 
    Svanella-Dumas L, Verdin E, Faure C, German-Retana S, Gognalons P et al. 2014. Adaptation of Lettuce mosaic virus to Catharanthus roseus involves mutations in the central domain of the VPg. Mol. Plant-Microbe Interact. 27:491–97
    [Google Scholar]
  145. 145. 
    Sytsma KJ, Litt A, Zjhra ML, Pires JC, Nepokroeff M et al. 2013. Clades, clocks, and continents: historical and biogeographical analysis of Myrtaceae, Vochysiaceae, and relatives in the Southern Hemisphere. Int. J. Plant Sci. 165:S85–105
    [Google Scholar]
  146. 146. 
    Tatineni S, Robertson CJ, Garnsey SM, Dawson WO 2011. A plant virus evolved by acquiring multiple nonconserved genes to extend its host range. PNAS 108:417366–71
    [Google Scholar]
  147. 147. 
    Thaxter R. 1891. The potato scab. Conn. Agric. Exp. Stn. Rep. 1890:81–95
    [Google Scholar]
  148. 148. 
    Thomma BPHJ, Nürnberger T, Joosten MHAJ 2011. Of PAMPs and effectors: the blurred PTI-ETI dichotomy. Plant Cell 23:4–15
    [Google Scholar]
  149. 149. 
    Thornhill AH, Ho SYW, Külheim C, Crisp MD 2015. Interpreting the modern distribution of Myrtaceae using a dated molecular phylogeny. Mol. Phylogenet. Evol. 93:29–43
    [Google Scholar]
  150. 150. 
    Thrall PH, Burdon JJ. 2003. Evolution of virulence in a plant host-pathogen metapopulation. Science 299:1735–37
    [Google Scholar]
  151. 151. 
    Vacher C, Piou D, Desprez-Loustau ML 2008. Architecture of an antagonistic tree/fungus network: the asymmetric influence of past evolutionary history. PLOS ONE 3:3e1740
    [Google Scholar]
  152. 152. 
    Valverde S, Elena SF, Solé R 2017. Spatially induced nestedness in a neutral model of phage-bacteria networks. Virus Evol 3:2vex021
    [Google Scholar]
  153. 153. 
    van Baarlen P, van Belkum A, Summerbell RC, Crous PW, Thomma BPHJ 2007. Molecular mechanisms of pathogenicity: How do pathogenic microorganisms develop cross-kingdom host jumps?. FEMS Microbiol. Rev. 31:239–77
    [Google Scholar]
  154. 154. 
    van Kan JAL, Shaw MW, Grant-Downton RT 2014. Botrytis species: relentless necrotrophic thugs or endophytes gone rogue?. Mol. Plant Pathol. 15:9957–61
    [Google Scholar]
  155. 155. 
    Vassilakos N, Simon V, Tzima A, Johansen E, Moury B 2016. Genetic determinism and evolutionary reconstruction of a host jump in a plant virus. Mol. Biol. Evol. 33:541–53
    [Google Scholar]
  156. 156. 
    Velásquez AC, Castroverde CDM, He S 2018. Plant-pathogen warfare under changing climate conditions. Curr. Biol. 28:R619–34
    [Google Scholar]
  157. 157. 
    Weitz JS, Poisot T, Meyer JR, Flores CO, Valverde S et al. 2013. Phage-bacteria infection networks. Trends Microbiol 21:82–91
    [Google Scholar]
  158. 158. 
    White JF, Reddy PV. 1998. Examination of structure and molecular phylogenetic relationships of some graminicolous symbionts in genera Epichloë and Parepichloë. Mycologia 90:226–34
    [Google Scholar]
  159. 159. 
    Whitfield AE, Falk BW, Rotenberg D 2015. Insect vector-mediated transmission of plant viruses. Virology 479:480278–89
    [Google Scholar]
  160. 160. 
    Wilkinson PA, Winfield MO, Barker GLA, Allen AM, Burridge A et al. 2012. CerealsDB 2.0: an integrated resource for plant breeders and scientists. BMC Bioinform 13:219
    [Google Scholar]
  161. 161. 
    Wright PE, Dyson HJ. 1999. Intrinsically unstructured proteins: reassessing the protein structure-function paradigm. J. Mol. Biol. 293:321–31
    [Google Scholar]
  162. 162. 
    Wu B, Melcher U, Guo X, Wang X, Fan L, Zhou G 2008. Assessment of codivergence of Mastreviruses with their plant hosts. BMC Evol. Biol. 8:335
    [Google Scholar]
  163. 163. 
    Zhao Y, Liang X, Zhou J-M 2018. Small RNA trafficking at the forefront of plant-pathogen interactions. F1000Research https://doi.org/10.12688/f1000research.15761.1
    [Crossref] [Google Scholar]
  164. 164. 
    Zhao Z, Liu H, Wang C, Xu J-R 2013. Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi. BMC Genom 14:274
    [Google Scholar]
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