Phytopathogen emergence in the genomics era

Trends in Plant Science

Volumn 20, Issue 4, 2015, Pages 246-255

  Thynne, Elisha ^a   McDonald, Megan C ^a   Solomon, Peter S ^a  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

Author keywords

Genome plasticity; Horizontal gene transfer; Hybridisation; Pathogen emergence

Indexed keywords

BACTERIAL PHENOMENA AND FUNCTIONS; FUNGUS; GENETICS; HORIZONTAL GENE TRANSFER; HOST PATHOGEN INTERACTION; HOST RANGE; MICROBIAL GENOME; MICROBIOLOGY; PHYSIOLOGY; PLANT DISEASE; VIRAL PHENOMENA AND FUNCTIONS; VIROLOGY;

BACTERIAL PHYSIOLOGICAL PHENOMENA; FUNGI; GENE TRANSFER, HORIZONTAL; GENOME, MICROBIAL; HOST SPECIFICITY; HOST-PATHOGEN INTERACTIONS; PLANT DISEASES; VIRUS PHYSIOLOGICAL PHENOMENA;

EID: 84926407786     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tplants.2015.01.009     Document Type: Review

References (105)

1. Anderson P.K., et al. Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnology drivers. Trends Ecol. Evol. 2004, 19:535-544.
2. Fisher M.C., et al. Emerging fungal threats to animal, plant and ecosystem health. Nature 2012, 484:186-194.
3. Dodds P.N., Rathjen J.P. Plant immunity: towards an integrated view of plant-pathogen interactions. Nat. Rev. Genet. 2010, 11:539-548.
4. Mayer K.F., et al. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 2014, 345:1251788.
5. Keeling P.J., Palmer J.D. Horizontal gene transfer in eukaryotic evolution. Nat. Rev. Genet. 2008, 9:605-618.
6. Raffaele S., Kamoun S. Genome evolution in filamentous plant pathogens: why bigger can be better. Nat. Rev. Microbiol. 2012, 10:417-430.
7. Ochman H., et al. Lateral gene transfer and the nature of bacterial innovation. Nature 2000, 405:299-304.
8. Andersson J.O. Lateral gene transfer in eukaryotes. Cell. Mol. Life Sci. 2005, 62:1182-1197.
9. Kirsch R., et al. Horizontal gene transfer and functional diversification of plant cell wall degrading polygalacturonases: key events in the evolution of herbivory in beetles. Insect Biochem. Mol. Biol. 2014, 52:33-50.
10. Slot J.C., Rokas A. Horizontal transfer of a large and highly toxic secondary metabolic gene cluster between fungi. Curr. Biol. 2011, 21:134-139.
11. Yin L-F., et al. Evolutionary analysis revealed the horizontal transfer of the Cyt b gene from Fungi to Chromista. Mol. Phylogenet. Evol. 2014, 76:155-161.
12. Gardiner D.M., et al. Cross-kingdom gene transfer facilitates the evolution of virulence in fungal pathogens. Plant Sci. 2013, 210:151-158.
13. Gardiner D.M., et al. Genomic analysis of Xanthomonas translucens pathogenic on wheat and barley reveals cross-kingdom gene transfer events and diverse protein delivery systems. PLoS ONE 2014, 9:e84995.
14. Jaramillo V.D., et al. Identification of horizontally transferred genes in the genus Colletotrichum reveals a steady tempo of bacterial to fungal gene transfer. BMC Genomics 2015, 16:2.
15. Jaramillo V.D.A., et al. Horizontal transfer of a subtilisin gene from plants into an ancestor of the plant pathogenic fungal genus Colletotrichum. PLoS ONE 2013, 8:e59078.
16. Klosterman S.J., et al. Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens. PLoS Pathog. 2011, 7:e1002137.
17. Lawrence D.P., et al. Interkingdom gene transfer of a hybrid NPS/PKS from bacteria to filamentous Ascomycota. PLoS ONE 2011, 6:e28231.
18. Nikolaidis N., et al. Plant expansins in bacteria and fungi: evolution by horizontal gene transfer and independent domain fusion. Mol. Biol. Evol. 2014, 31:376-386.
19. Richards T.A., et al. Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:15258-15263.
20. Sun B-F., et al. Multiple interkingdom horizontal gene transfers in Pyrenophora and closely related species and their contributions to phytopathogenic lifestyles. PLoS ONE 2013, 8:e60029.
21. 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. U.S.A. 2012, 109:5110-5115.
22. Richards T.A., et al. Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi. Plant Cell Online 2009, 21:1897-1911.
23. Hacker J., Kaper J.B. Pathogenicity islands and the evolution of microbes. Annu. Rev. Microbiol. 2000, 54:641-679.
24. Juhas M., et al. Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol. Rev. 2009, 33:376-393.
25. Huguet-Tapia J.C., Loria R. Draft genome sequence of Streptomyces acidiscabies 84-104, an emergent plant pathogen. J. Bacteriol. 2012, 194:1847.
26. Mann R.A., et al. Comparative analysis of the Hrp pathogenicity island of Rubus-and Spiraeoideae-infecting Erwinia amylovora strains identifies the IT region as a remnant of an integrative conjugative element. Gene 2012, 504:6-12.
27. Kerff F., et al. Crystal structure and activity of Bacillus subtilis YoaJ (EXLX1), a bacterial expansin that promotes root colonization. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:16876-16881.
28. Cosgrove D.J. Loosening of plant cell walls by expansins. Nature 2000, 407:321-326.
29. Hu J., et al. Genomic characterization of the conditionally dispensable chromosome in Alternaria arborescens provides evidence for horizontal gene transfer. BMC Genomics 2012, 13:171.
30. Ma L-J., et al. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 2010, 464:367-373.
31. Friesen T.L., et al. Emergence of a new disease as a result of interspecific virulence gene transfer. Nat. Genet. 2006, 38:953-956.
32. Gardiner D.M., et al. Comparative pathogenomics reveals horizontally acquired novel virulence genes in fungi infecting cereal hosts. PLoS Pathog. 2012, 8:e1002952.
33. Giraud T., et al. Speciation in fungi. Fungal Genet. Biol. 2008, 45:791-802.
34. Stukenbrock E.H., et al. Origin and domestication of the fungal wheat pathogen Mycosphaerella graminicola via sympatric speciation. Mol. Biol. Evol. 2007, 24:398-411.
35. Stukenbrock E.H., et al. Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species. Proc. Natl. Acad. Sci. U.S.A. 2012, 109:10954-10959.
36. Inderbitzin P., et al. The ascomycete Verticillium longisporum is a hybrid and a plant pathogen with an expanded host range. PLoS ONE 2011, 6:e18260.
37. Karapapa V., et al. Morphological and molecular characterization of Verticillium longisporum comb. nov. pathogenic to oilseed rape. Mycol. Res. 1997, 101:1281-1294.
38. Collado-Romero M., et al. DNA sequence analysis of conserved genes reveals hybridization events that increase genetic diversity in Verticillium dahliae. Fungal Biol. 2010, 114:209-218.
39. Bertier L., et al. Host adaptation and speciation through hybridization and polyploidy in Phytophthora. PLoS ONE 2013, 8:e85385.
40. Goss E.M., et al. The plant pathogen Phytophthora andina emerged via hybridization of an unknown Phytophthora species and the Irish potato famine pathogen, P. Infestans. PLoS ONE 2011, 6:e24543.
41. Hüberli D., et al. Fishing for Phytophthora from Western Australia's waterways: a distribution and diversity survey. Aust. Plant Pathol. 2013, 42:251-260.
42. Nagel J.H., et al. Characterization of Phytophthora hybrids from ITS clade 6 associated with riparian ecosystems in South Africa and Australia. Fungal Biol. 2013, 117:329-347.
43. Nechwatal J., Lebecka R. Genetic and phenotypic analyses of Pythium isolates from reed suggest the occurrence of a new species, P. phragmiticola, and its involvement in the generation of a natural hybrid. Mycoscience 2014, 55:134-143.
44. Oh E., et al. Surveys of soil and water reveal a goldmine of Phytophthora diversity in south African natural ecosystems. IMA Fungus 2013, 4:123.
45. Oliver R.P., Solomon P.S. Recent fungal diseases of crop plants: is lateral gene transfer a common theme?. Mol. Plant Microbe Interact. 2008, 21:287-293.
46. Vernikos G., et al. Ten years of pan-genome analyses. Curr. Opin. Microbiol. 2015, 23:148-154.
47. Adhikari B.N., et al. Comparative genomics reveals insight into virulence strategies of plant pathogenic oomycetes. PLoS ONE 2013, 8:e75072.
48. Ohm R.A., et al. Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathog. 2012, 8:e1003037.
49. Baltrus D.A., et al. Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 Pseudomonas syringae isolates. PLoS Pathog. 2011, 7:e1002132.
50. de Jonge R., et al. Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen. Genome Res. 2013, 23:1271-1282.
51. Jalan N., et al. Comparative genomic analysis of Xanthomonas axonopodis pv. citrumelo F1, which causes citrus bacterial spot disease, and related strains provides insights into virulence and host specificity. J. Bacteriol. 2011, 193:6342-6357.
52. Manning V.A., et al. Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence. G3: Genes Genomes Genet. 2013, 3:41-63.
53. Yoshida K., et al. Association genetics reveals three novel avirulence genes from the rice blast fungal pathogen Magnaporthe oryzae. Plant Cell Online 2009, 21:1573-1591.
54. Syme R.A., et al. Resequencing and comparative genomics of Stagonospora nodorum: sectional gene absence and effector discovery. G3: Genes Genomes Genet. 2013, 3:959-969.
55. Benson D.A., et al. GenBank. Nucleic Acids Res. 2012, 40:D48-D53.
56. Benson D.A., et al. GenBank. Nucleic Acids Res. 2006, 34:D16-D20.
57. Goss E.M., et al. The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes. Proc. Natl. Acad. Sci. U.S.A. 2014, 201401884.
58. McDonald M.C., et al. Phylogenetic and population genetic analyses of Phaeosphaeria nodorum and its close relatives indicate cryptic species and an origin in the Fertile Crescent. Fungal Genet. Biol. 2012, 49:882-895.
59. Ames M., Spooner D.M. DNA from herbarium specimens settles a controversy about origins of the European potato. Am. J. Bot. 2008, 95:252-257.
60. Yoshida K., et al. Mining herbaria for plant pathogen genomes: back to the future. PLoS Pathog. 2014, 10:e1004028.
61. Yoshida K., et al. The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. Elife 2013, 2:e00731.
62. Sutton B.C., Marasas W.F.O. Observations on Neottiosporina and Tiarosporella. Trans. Br. Mycol. Soc. 1976, 67:69-76.
63. Slippers B., Wingfield M.J. Botryosphaeriaceae as endophytes and latent pathogens of woody plants: diversity, ecology and impact. Fungal Biol. Rev. 2007, 21:90-106.
64. Crous P.W., et al. Phylogenetic lineages in the Botryosphaeriaceae. Stud. Mycol. 2006, 55:235-253.
65. Phillips A., et al. The Botryosphaeriaceae: genera and species known from culture. Stud. Mycol. 2013, 76:51-167.
66. Jami F., et al. Five new species of the Botryosphaeriaceae from Acacia Karroo in South Africa. Cryptogamie Mycol. 2012, 33:245-266.
67. Jami F., et al. Botryosphaeriaceae species overlap on four unrelated, native South African hosts. Fungal Biol. 2014, 118:168-179.
68. Monteil C.L., et al. Nonagricultural reservoirs contribute to emergence and evolution of Pseudomonas syringae crop pathogens. New Phytol. 2013, 199:800-811.
69. Aly A.H., et al. Fungal endophytes from higher plants: a prolific source of phytochemicals and other bioactive natural products. Fungal Divers. 2010, 41:1-16.
70. Jami F., et al. Greater Botryosphaeriaceae diversity in healthy than associated diseased Acacia karroo tree tissues. Aust. Plant Pathol. 2013, 42:421-430.
71. Slippers B., et al. Phylogenetic lineages in the Botryosphaeriales: a systematic and evolutionary framework. Stud. Mycol. 2013, 76:31-49.
72. Alvarez-Loayza P., et al. Light converts endosymbiotic fungus to pathogen, influencing seedling survival and niche-space filling of a common tropical tree, Iriartea deltoidea. PLoS ONE 2011, 6:e16386.
73. Delaye L., et al. Endophytes versus biotrophic and necrotrophic pathogens - are fungal lifestyles evolutionarily stable traits?. Fungal Divers. 2013, 60:125-135.
74. Ryan R.P., et al. Pathogenomics of Xanthomonas: understanding bacterium-plant interactions. Nat. Rev. Microbiol. 2011, 9:344-355.
75. Scortichini M., et al. Pseudomonas syringae pv. actinidiae: a re-emerging, multi-faceted, pandemic pathogen. Mol. Plant Pathol. 2012, 13:631-640.
76. Chapman J., et al. Phylogenetic relationships among global populations of Pseudomonas syringae pv. actinidiae. Phytopathology 2012, 102:1034-1044.
77. Marcelletti S., et al. Pseudomonas syringae pv. actinidiae draft genomes comparison reveal strain-specific features involved in adaptation and virulence to Actinidia species. PLoS ONE 2011, 6:e27297.
78. McCann H.C., et al. Genomic analysis of the kiwifruit pathogen Pseudomonas syringae pv. actinidiae provides insight into the origins of an emergent plant disease. PLoS Pathog. 2013, 9:e1003503.
79. Morris C., et al. Inferring the evolutionary history of the plant pathogen Pseudomonas syringae from its biogeography in headwaters of rivers in North America, Europe, and New Zealand. MBio 2010, 1:e00107-e00110.
80. Morris C.E., et al. The life history of the plant pathogen Pseudomonas syringae is linked to the water cycle. ISME J. 2008, 2:321-334.
81. Dean R., et al. The Top 10 fungal pathogens in molecular plant pathology. Mol. Plant Pathol. 2012, 13:414-430.
82. Dean R.A., et al. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature 2005, 434:980-986.
83. Valent B., Khang C.H. Recent advances in rice blast effector research. Curr. Opin. Plant Biol. 2010, 13:434-441.
84. Kohli M., et al. Pyricularia blast - a threat to wheat cultivation. Czech J. Genet. Plant Breed. 2011, 47:S130-S134.
85. Van Vu B., et al. Cellulases belonging to glycoside hydrolase families 6 and 7 contribute to the virulence of Magnaporthe oryzae. Mol. Plant Microbe Interact. 2012, 25:1135-1141.
86. Maciel J.L.N., et al. Population structure and pathotype diversity of the wheat blast pathogen Magnaporthe oryzae 25 years after its emergence in Brazil. Phytopathology 2014, 104:95-107.
87. Pratt K. UK researchers find important new disease. UKAgNews 2012, 24 April.
88. Tosa Y., et al. Genetic constitution and pathogenicity of Lolium isolates of Magnaporthe oryzae in comparison with host species-specific pathotypes of the blast fungus. Phytopathology 2004, 94:454-462.
89. Gross A., et al. Hymenoscyphus pseudoalbidus, the causal agent of European ash dieback. Mol. Plant Pathol. 2014, 15:5-21.
90. Queloz V., et al. Cryptic speciation in Hymenoscyphus albidus. For. Pathol. 2011, 41:133-142.
91. Chandelier A., et al. First report of the ash dieback pathogen Hymenoscyphus pseudoalbidus (Anamorph Chalara fraxinea) on Fraxinus excelsior in Belgium. Plant Dis. 2011, 95:220.
92. Husson C., et al. Chalara fraxinea is an invasive pathogen in France. Eur. J. Plant Pathol. 2011, 130:311-324.
93. McKinney L.V., et al. Rapid invasion by an aggressive pathogenic fungus Hymenoscyphus pseudoalbidus replaces a native decomposer Hymenoscyphus albidus: a case of local cryptic extinction?. Fungal Ecol. 2012, 5:663-669.
94. Zhao Y-J., et al. Hymenoscyphus pseudoalbidus, the correct name for Lambertella albida reported from Japan. Mycotaxon 2013, 122:25-41.
95. Gross A., et al. Population structure of the invasive forest pathogen Hymenoscyphus pseudoalbidus. Mol. Ecol. 2014, 23:2943-2960.
96. Zheng H-D., Zhuang W-Y. Hymenoscyphus albidoides sp. nov. and H. pseudoalbidus from China. Mycol. Prog. 2013, 1-14.
97. Gherghel F., et al. The development of a species-specific test to detect Hymenoschyphus pseudoalbidus in ash tissues. For. Pathol. 2014, 44:137-144.
98. Gross A., et al. A molecular toolkit for population genetic investigations of the ash dieback pathogen Hymenoscyphus pseudoalbidus. For. Pathol. 2012, 42:252-264.
99. Gabriela Roca M., et al. Conidial anastomosis tubes in filamentous fungi. FEMS Microbiol. Lett. 2005, 249:191-198.
100. Richards T.A., et al. Gene transfer into the fungi. Fungal Biol. Rev. 2011, 25:98-110.
101. Ishikawa F.H., et al. Heterokaryon incompatibility is suppressed following conidial anastomosis tube fusion in a fungal plant pathogen. PLoS ONE 2012, 7:e31175.
102. Medini D., et al. The microbial pan-genome. Curr. Opin. Genet. Dev. 2005, 15:589-594.
103. Tettelin H., et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial 'pan-genome'. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:13950-13955.
104. Nguyen N., et al. Building a pan-genome reference for a population. J. Comput. Biol. 2015, 22:1-15.
105. Bankevich A., et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 2012, 19:455-477.