Population-level deep sequencing reveals the interplay of clonal and sexual reproduction in the fungal wheat pathogen Open Access

Abstract

Pathogens cause significant challenges to global food security. On annual crops, pathogens must re-infect from environmental sources in every growing season. Fungal pathogens have evolved mixed reproductive strategies to cope with the distinct challenges of colonizing growing plants. However, how pathogen diversity evolves during growing seasons remains largely unknown. Here, we performed a deep hierarchical sampling in a single experimental wheat field infected by the major fungal pathogen . We analysed whole genome sequences of 177 isolates collected from 12 distinct cultivars replicated in space at three time points of the growing season to maximize capture of genetic diversity. The field population was highly diverse with 37 SNPs per kilobase, a linkage disequilibrium decay within 200–700 bp and a high effective population size. Using experimental infections, we tested a subset of the collected isolates on the dominant cultivar planted in the field. However, we found no significant difference in virulence of isolates collected from the same cultivar compared to isolates collected on other cultivars. About 20 % of the isolate genotypes were grouped into 15 clonal groups. Pairs of clones were disproportionally found at short distances (<5 m), consistent with experimental estimates for per-generation dispersal distances performed in the same field. This confirms predominant leaf-to-leaf transmission during the growing season. Surprisingly, levels of clonality did not increase over time in the field although reproduction is thought to be exclusively asexual during the growing season. Our study shows that the pathogen establishes vast and stable gene pools in single fields. Monitoring short-term evolutionary changes in crop pathogens will inform more durable strategies to contain diseases.

Funding
This study was supported by the:
  • schweizerischer nationalfonds zur förderung der wissenschaftlichen forschung (Award 31003A_173265)
    • Principle Award Recipient: DanielCroll
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2021-10-07
2024-03-29
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References

  1. Gandon S, Hochberg ME, Holt RD, Day T. What limits the evolutionary emergence of pathogens? Philosophical transactions of the Royal Society B: biological sciences; 2013; 36820120086
  2. Read AF, Taylor LH. The ecology of genetically diverse infections. Science 2001; 292:1099–1102 [View Article] [PubMed]
    [Google Scholar]
  3. Thrall PH, Burdon JJ. Evolution of virulence in a plant host-pathogen metapopulation. Science 2003; 299:1735–1737 [View Article] [PubMed]
    [Google Scholar]
  4. Vignuzzi M, Stone JK, Arnold JJ, Cameron CE, Andino R. Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population. Nature 2006; 439:344–348 [View Article] [PubMed]
    [Google Scholar]
  5. Hamelin FM, Castel M, Poggi S, Andrivon D, Mailleret L. Seasonality and the evolutionary divergence of plant parasites. Ecology 2011; 92:2159–2166 [View Article] [PubMed]
    [Google Scholar]
  6. Linde CC. Population genetic analyses of plant pathogens: new challenges and opportunities. Australasian Plant Pathology 2010; 39:23–28 [View Article]
    [Google Scholar]
  7. Walther BA, Ewald PW. Pathogen survival in the external environment and the evolution of virulence. Biol Rev Camb Philos Soc 2004; 79:849–869 [View Article] [PubMed]
    [Google Scholar]
  8. He DC, Zhan JS, Xie LH. Problems, challenges and future of plant disease management: from an ecological point of view. J Integr Agric 2016; 15:705–715
    [Google Scholar]
  9. Sundin GW, Castiblanco LF, Yuan X, Zeng Q, Yang C-H. Bacterial disease management: challenges, experience, innovation and future prospects: challenges in bacterial molecular plant pathology. Mol Plant Pathol 2016; 17:1506–1518 [View Article] [PubMed]
    [Google Scholar]
  10. Laine A.‐L., Barrès B. Epidemiological and evolutionary consequences of life‐history trade‐offs in pathogens. Plant Pathol 2013; 62:96–105 [View Article]
    [Google Scholar]
  11. Mariette N, Mabon R, Corbière R, Boulard F, Glais I et al. Phenotypic and genotypic changes in French populations of Phytophthora infestans : are invasive clones the most aggressive?. Plant Pathol 2016; 65:577–586 [View Article]
    [Google Scholar]
  12. Becheler R, Xhaard C, Klein EK, Hayden KJ, Frey P et al. Genetic signatures of a range expansion in natura: when clones play leapfrog. Ecol Evol 2016; 6:6625–6632 [View Article] [PubMed]
    [Google Scholar]
  13. Tack AJM, Thrall PH, Barrett LG, Burdon JJ, Laine AL. Variation in infectivity and aggressiveness in space and time in wild host-pathogen systems: Causes and consequences. J Evol Biol 2012; 25:1918–1936 [View Article] [PubMed]
    [Google Scholar]
  14. Barrett LG, Thrall PH, Burdon JJ, Linde CC. Life history determines genetic structure and evolutionary potential of host-parasite interactions. Trends Ecol Evol (Amst) 2008; 23:678–685 [View Article] [PubMed]
    [Google Scholar]
  15. Burdon JJ, Zhan J, Barrett LG, Papaix J, Thrall PH. Addressing the challenges of pathogen evolution on the world’s arable crops. Phytopathology 2016; 106:1117–1127 [View Article] [PubMed]
    [Google Scholar]
  16. Suffert F, Delestre G, Gélisse S. Sexual reproduction in the fungal foliar pathogen Zymoseptoria tritici is driven by antagonistic density dependence mechanisms. Microb Ecol 2019; 77:110–123 [View Article] [PubMed]
    [Google Scholar]
  17. Dodds P, Thrall P. Recognition events and host-pathogen co-evolution in gene-for-gene resistance to flax rust. Funct Plant Biol 2009; 36:395–408 [View Article] [PubMed]
    [Google Scholar]
  18. Jones JDG, Dangl JL. The plant immune system. Nature 2006; 444:323–329 [View Article] [PubMed]
    [Google Scholar]
  19. Nomura K, DebRoy S, Lee YH, Pumplin N, Jones J et al. A bacterial virulence protein suppresses host innate immunity to cause plant disease. Science 2006; 313:220–223 [View Article] [PubMed]
    [Google Scholar]
  20. Sun W, Dunning FM, Pfund C, Weingarten R, Bent AF. Within-species flagellin polymorphism in Xanthomonas campestris pv campestris and its impact on elicitation of Arabidopsis FLAGELLIN SENSING2-dependent defenses. Plant Cell 2006; 18:764–779 [View Article] [PubMed]
    [Google Scholar]
  21. De Torres M, Mansfield JW, Grabov N, Brown IR, Ammouneh H et al. Pseudomonas syringae effector AvrPtoB suppresses basal defence in Arabidopsis. Plant J 2006; 47:368–382 [View Article] [PubMed]
    [Google Scholar]
  22. Chisholm ST, Coaker G, Day B, Staskawicz BJ. Host-microbe interactions: Shaping the evolution of the plant immune response. Cell 2006; 124:803–814 [View Article] [PubMed]
    [Google Scholar]
  23. Steinberg G. Cell biology of Zymoseptoria tritici: Pathogen cell organization and wheat infection. Fungal Genet Biol 2015; 79:17–23 [View Article] [PubMed]
    [Google Scholar]
  24. Parratt SR, Numminen E, Laine A-L. Infectious disease dynamics in heterogeneous landscapes. Annu Rev Ecol Evol Syst 2016; 47:283–306 [View Article]
    [Google Scholar]
  25. Peay KG, Bruns TD. Spore dispersal of basidiomycete fungi at the landscape scale is driven by stochastic and deterministic processes and generates variability in plant-fungal interactions. New Phytol 2014; 204:180–191 [View Article] [PubMed]
    [Google Scholar]
  26. Susi H, Burdon JJ, Thrall PH, Nemri A, Barrett LG. Genetic analysis reveals long-standing population differentiation and high diversity in the rust pathogen melampsora lini. PLoS Pathog 2020; 16:e1008731 [View Article] [PubMed]
    [Google Scholar]
  27. Billiard S, López-Villavicencio M, Hood ME, Giraud T. Sex, outcrossing and mating types: Unsolved questions in fungi and beyond. J Evol Biol 2012; 25:1020–1038 [View Article] [PubMed]
    [Google Scholar]
  28. McDonald BA. The population genetics of fungi: tools and techniques. Phytopathology 1997; 87:448–453 [View Article] [PubMed]
    [Google Scholar]
  29. McDonald BA, Linde C. Pathogen population genetics, evolutionary potential, and durable resistance. Annu Rev Phytopathol 2002; 40:349–379 [View Article] [PubMed]
    [Google Scholar]
  30. Fones H, Gurr S. The impact of Septoria tritici Blotch disease on wheat: An EU perspective. Fungal Genet Biol 2015; 79:3–7 [View Article] [PubMed]
    [Google Scholar]
  31. Hartmann FE, Croll D. Distinct trajectories of massive recent gene gains and losses in populations of a microbial eukaryotic pathogen. Mol Biol Evol 2017; 34:2808–2822 [View Article] [PubMed]
    [Google Scholar]
  32. Hartmann FE, Sánchez-Vallet A, McDonald BA, Croll D. A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements. ISME J 2017; 11:1189–1204 [View Article] [PubMed]
    [Google Scholar]
  33. Krishnan P, Ma X, McDonald BA, Brunner PC. Widespread signatures of selection for secreted peptidases in a fungal plant pathogen. BMC Evol Biol 2018; 18:7 [View Article] [PubMed]
    [Google Scholar]
  34. Zhong Z, Marcel TC, Hartmann FE, Ma X, Plissonneau C et al. A small secreted protein in Zymoseptoria tritici is responsible for avirulence on wheat cultivars carrying the Stb6 resistance gene. New Phytol 2017; 214:619–631 [View Article] [PubMed]
    [Google Scholar]
  35. Chen R-S, Mcdonald BA. Sexual reproduction plays a major role in the genetic structure of populations of the fungus Mycosphaerella graminicola; 1996
  36. Kema GH, Verstappen EC, Todorova M, Waalwijk C. Successful crosses and molecular tetrad and progeny analyses demonstrate heterothallism in Mycosphaerella graminicola. Curr Genet 1996; 30:251–258 [View Article] [PubMed]
    [Google Scholar]
  37. Zhan J, Pettway RE, McDonald BA. The global genetic structure of the wheat pathogen Mycosphaerella graminicola is characterized by high nuclear diversity, low mitochondrial diversity, regular recombination, and gene flow. Fungal Genet Biol 2003; 38:286–297 [View Article] [PubMed]
    [Google Scholar]
  38. Hartmann FE, McDonald BA, Croll D. Genome-wide evidence for divergent selection between populations of a major agricultural pathogen. Mol Ecol 2018; 27:2725–2741 [View Article] [PubMed]
    [Google Scholar]
  39. McDonald MC, Renkin M, Spackman M, Orchard B, Croll D et al. Rapid parallel evolution of azole fungicide resistance in Australian populations of the wheat pathogen Zymoseptoria tritici. Appl Environ Microbiol 2019; 85:e01908-18 [View Article] [PubMed]
    [Google Scholar]
  40. Suffert F, Goyeau H, Sache I, Carpentier F, Gélisse S et al. Epidemiological trade-off between intra- and interannual scales in the evolution of aggressiveness in a local plant pathogen population. Evol Appl 2018; 11:768–780 [View Article] [PubMed]
    [Google Scholar]
  41. Morais D, Duplaix C, Sache I, Laval V, Suffert F et al. Overall stability in the genetic structure of a Zymoseptoria tritici population from epidemic to interepidemic stages at a small spatial scale. Eur J Plant Pathol 2019; 154:423–436 [View Article]
    [Google Scholar]
  42. Linde CC, Zhan J, McDonald BA. Population structure of Mycosphaerella graminicola: From lesions to continents. Phytopathology 2002; 92:946–955 [View Article] [PubMed]
    [Google Scholar]
  43. Kirchgessner N, Liebisch F, Yu K, Pfeifer J, Friedli M et al. The ETH field phenotyping platform FIP: a cable-suspended multi-sensor system. Functional Plant Biol. 2017; 44:154–168 [View Article]
    [Google Scholar]
  44. Levy L, Courvoisier N, Rechsteiner S, Herrera J, Brabant C. Winterweizen: Bilanz AUS 15 Jahren Sortenprüfung unter extensiven Anbaubedingungen. Agrarforschung Schweiz 2017; 8:300–309
    [Google Scholar]
  45. Singh NK, Badet T, Abraham L, Croll D. Rapid sequence evolution driven by transposable elements at a virulence locus in a fungal wheat pathogen. BMC Genomics 2021; 22:393 [View Article] [PubMed]
    [Google Scholar]
  46. Karisto P, Hund A, Yu K, Anderegg J, Walter A et al. Ranking quantitative resistance to septoria tritici blotch in elite wheat cultivars using automated image analysis. Phytopathology 2018; 108:568–581 [View Article] [PubMed]
    [Google Scholar]
  47. Oggenfuss U, Badet T, Wicker T, Hartmann FE, Singh NK. A population-level invasion by transposable. bioRxiv 2020
    [Google Scholar]
  48. Andrews S. FastQC: A Quality Control Tool for High Throughput Sequence Data. www.bioinformatics.babraham.ac.uk/projects/fastqc
  49. Bolger AM, Lohse M, Usadel B. Trimmomatic: a Flexible Trimmer for Illumina Sequence Data Bioinformatics (Oxford, England: 2014 pp 2114–2120
    [Google Scholar]
  50. Goodwin SB, Ben MS, Dhillon B, Wittenberg AHJ, Crane CF et al. Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis (HS Malik, Ed.). PLoS Genet 2011; 7:e1002070 [View Article] [PubMed]
    [Google Scholar]
  51. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012; 9:357–359 [View Article] [PubMed]
    [Google Scholar]
  52. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010; 20:1297–1303 [View Article] [PubMed]
    [Google Scholar]
  53. Danecek P, Auton A, Abecasis G, Albers CA, Banks E et al. The variant call format and VCFtools. Bioinformatics 2011; 27:2156–2158 [View Article] [PubMed]
    [Google Scholar]
  54. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR et al. PLINK: A tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007; 81:559–575 [View Article] [PubMed]
    [Google Scholar]
  55. Wickham H. Ggplot2: Elegant Graphics for Data Analysis Springer-Verlag New York; 2016
    [Google Scholar]
  56. Ingvarsson PK. Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., salicaceae). Genetics 2005; 169:945–953 [View Article] [PubMed]
    [Google Scholar]
  57. Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR et al. Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci U S A 2001; 98:11479–11484 [View Article]
    [Google Scholar]
  58. Knaus BJ, Grünwald NJ. VCFR: A Package to Manipulate and Visualize Variant Call Format Data in R John Wiley & Sons, Ltd; 2017 pp 44–53
    [Google Scholar]
  59. Dray S, Dufour A-B. The ade4 package: Implementing the duality diagram for ecologists. J Stat Softw 2007; 22:1–20 [View Article]
    [Google Scholar]
  60. Huson DH. SplitsTree: Analyzing and visualizing evolutionary data. Bioinformatics 1998; 14:68–73 [View Article] [PubMed]
    [Google Scholar]
  61. Paradis E, Schliep K. Ape 5.0: An environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 2019; 35:526–528 [View Article] [PubMed]
    [Google Scholar]
  62. Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P. Package ‘vegan’ Title Community Ecology Package Version 2.5-6 2019
    [Google Scholar]
  63. Santiago E, Novo I, Pardiñas AF, Saura M, Wang J et al. Recent demographic history inferred by high-resolution analysis of linkage Disequilibrium. Mol Biol Evol 2020; 37:3642–3653 [View Article] [PubMed]
    [Google Scholar]
  64. Croll D, Lendenmann MH, Stewart E, McDonald BA. The impact of recombination hotspots on genome evolution of a fungal plant pathogen. Genetics 2015; 201:1213–1228 [View Article] [PubMed]
    [Google Scholar]
  65. Karisto P, Suffert F, Mikaberidze A. Measuring splash-dispersal of a major wheat pathogen in the field. PhytoFrontiers™ 2021 [View Article]
    [Google Scholar]
  66. Harris CR, Millman KJ, van der Walt SJ, Gommers R, Virtanen P et al. Array programming with NumPy. Nature 2020; 585:357–362 [View Article] [PubMed]
    [Google Scholar]
  67. Virtanen P, Gommers R, Oliphant TE, Haberland M, Reddy T et al. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat Methods 2020; 17:261–272 [View Article] [PubMed]
    [Google Scholar]
  68. Mckinney W. Data structures for statistical computing in python; 2010
  69. Hunter JD. Matplotlib: a 2D graphics environment. Comput Sci Eng 2007; 9:90–95 [View Article]
    [Google Scholar]
  70. Meier U. Growth stages of mono-and dicotyledonous plants BBCH monograph edited by Uwe Meier federal biological research centre for agriculture and forestry; 2001
  71. Croll D, McDonald BA. The accessory genome as a cradle for adaptive evolution in pathogens. PLoS Pathog 2012; 8:e1002608 [View Article] [PubMed]
    [Google Scholar]
  72. Stukenbrock EH, Jørgensen FG, Zala M, Hansen TT, McDonald BA et al. Whole-genome and chromosome evolution associated with host adaptation and speciation of the wheat pathogen Mycosphaerella graminicola (HS Malik, Ed.). PLoS Genet 2010; 6:e1001189 [View Article] [PubMed]
    [Google Scholar]
  73. Schotanus K, Soyer JL, Connolly LR, Grandaubert J, Happel P et al. Histone modifications rather than the novel regional centromeres of Zymoseptoria tritici distinguish core and accessory chromosomes. Epigenetics Chromatin 2015; 8:41 [View Article] [PubMed]
    [Google Scholar]
  74. Badet T, Fouché S, Hartmann FE, Croll D. Machine-learning predicts genomic determinants of meiosis-driven structural variation in a eukaryotic pathogen. bioRxiv 20202020
    [Google Scholar]
  75. Barton NH. Genetic linkage and natural selection. Philosophical transactions of the Royal Society B: biological sciences; 2010; 3652559–2569
  76. Slatkin M. Linkage disequilibrium--understanding the evolutionary past and mapping the medical future. Nat Rev Genet 2008; 9:477–485 [View Article] [PubMed]
    [Google Scholar]
  77. Stukenbrock EH, McDonald BA. The origins of plant pathogens in agro-ecosystems. Annu Rev Phytopathol 2008; 46:75–100 [View Article]
    [Google Scholar]
  78. Badet T, Oggenfuss U, Abraham L, McDonald BA, Croll D. A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici. BMC Biol 2020; 18:12 [View Article]
    [Google Scholar]
  79. Daverdin G, Rouxel T, Gout L, Aubertot JN, Fudal I et al. Genome Structure and Reproductive Behaviour Influence the Evolutionary Potential of a Fungal Phytopathogen (A Andrianopoulos, Ed.). PLoS Pathog 2012; 8:e1003020 [View Article] [PubMed]
    [Google Scholar]
  80. Persoons A, Hayden KJ, Fabre B, Frey P, De Mita S et al. The escalatory Red Queen: Population extinction and replacement following arms race dynamics in poplar rust. Mol Ecol 2017; 26:1902–1918 [View Article] [PubMed]
    [Google Scholar]
  81. Kerdraon L, Laval V, Suffert F. Microbiomes and pathogen survival in crop residues, an ecotone between plant and soil. Phytobiomes J 2019; 3:246–255 [View Article]
    [Google Scholar]
  82. Barrès B, Carlier J, Seguin M, Fenouillet C, Cilas C et al. Understanding the recent colonization history of a plant pathogenic fungus using population genetic tools and Approximate Bayesian Computation. Heredity (Edinb) 2012; 109:269–279 [View Article] [PubMed]
    [Google Scholar]
  83. Suffert F, Ravigné V, Sachec I. Seasonal changes drive short-term selection for fitness traits in the wheat pathogen Zymoseptoria tritici. Appl Environ Microbiol 2015; 81:6367–6379 [View Article] [PubMed]
    [Google Scholar]
  84. Dutta A, Hartmann FE, Francisco CS, McDonald BA, Croll D. Mapping the adaptive landscape of a major agricultural pathogen reveals evolutionary constraints across heterogeneous environments. ISME J 20211–18
    [Google Scholar]
  85. Hassine M, Siah A, Hellin P, Cadalen T, Halama P et al. Sexual reproduction of Zymoseptoria tritici on durum wheat in Tunisia revealed by presence of airborne inoculum, fruiting bodies and high levels of genetic diversity. Fungal Biol 2019; 123:763–772 [View Article] [PubMed]
    [Google Scholar]
  86. Siah A, Bomble M, Tisserant B, Cadalen T, Holvoet M et al. Genetic structure of Zymoseptoria tritici in northern France at region, field, plant, and leaf layer scales. Phytopathology 2018; 108:1114–1123 [View Article] [PubMed]
    [Google Scholar]
  87. Drenth A, McTaggart AR, Wingfield BD. Fungal clones win the battle, but recombination wins the war. IMA Fungus 2019; 10:18 [View Article] [PubMed]
    [Google Scholar]
  88. Möller M, Stukenbrock EH. Evolution and genome architecture in fungal plant pathogens. Nat Rev Microbiol 2017; 15:756–771
    [Google Scholar]
  89. Burdon JJ, Silk J. Sources and patterns of diversity in plant-pathogenic fungi. Phytopathology 1997; 87:664–669 [View Article] [PubMed]
    [Google Scholar]
  90. Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC et al. Emerging fungal threats to animal, plant and ecosystem health. Nature 2012; 484:186–194 [View Article] [PubMed]
    [Google Scholar]
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