Population genomics ofMacrophominaspp. reveals cryptic host specialization and evidence for meiotic recombination

  1. K.K. Pennerman
  2. P. Goldman
  3. C.J. Dilla-Ermita
  4. G. Ramos
  5. J.H. Jaime
  6. J. Lopez-Hernandez
  7. J. Ramos
  8. M. Aviles
  9. C. Borrero
  10. A.O. Gomez
  11. J.M. Neal
  12. M. Chilvers
  13. V. Ortiz
  14. E.H. Stukenbrock
  15. G.H. Goldman
  16. A. Mengitsu
  17. H.D. Lopez-Nicora
  18. G.O. Sacher
  19. N. Vaghefi
  20. L. Kiss
  21. J.P. Benz
  22. A.R. Machado
  23. T.E. Seijo
  24. N.A. Peres
  25. F.N. Martin
  26. J.C. Broome
  27. K. Ivors
  28. G. Cole
  29. S. Knapp
  30. D.J. McFarlane
  31. S.W. Mattner
  32. M. Gambardella
  33. P.M. Henry
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Abstract

Knowledge of the factors structuring populations of pathogenic fungi is fundamental to disease management efforts and basic biology. High-quality short-read sequence data were obtained for 463Macrophominaspp. isolates collected from 91 host plant species and soil in 23 countries. Analyses revealed high diversity, admixture, and equal mating type ratios suggesting on-going recombination. Although most tested isolates could asymptomatically colonize strawberry, only isolates from a single phylogroup caused disease. In addition to strawberry, evidence for host specialization was discovered for soybean, demonstrating this broad host range pathogen contains phylogroups with cryptic specialization. Geography × isolate genotype associations were weak, suggesting these species were frequently trafficked between regions. Re-analysis using genomic data supported current species boundaries, and new molecular markers were designed to specifically identify each species. Contrary to expectations,M. phaseolinashould be considered a species with both specialist and generalist populations for which meiosis can increase genetic diversity.

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