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Research

Our current research focuses on studying the biology and control of exotic and reemerging Phytophthora diseases with a particular emphasis on the Sudden Oak Death pathogen, P. ramorum and the Irish famine pathogen P. infestans. We are particularly interested in understanding how pathogens evolve and adapt. Our research includes the following broad objectives:

1. Determine pattern and process of Phytophthora spp. emergence [1][2][3][4];

2. Comparative and population genomics of Phytophthora spp. [5][6][7];

4. Development of computational tools for population genetics, genomics and metabarcoding [8][9] [10][11][12] (Github)

5. Metabarcoding to characterize the microbiome associated with plants [11];

6. Phytophthora community ecology [13][14]; and

7. Development of systems approaches for management of Phytophthora diseases [15].


References

  1. Grünwald NJ, Garbelotto M, Goss EM, Heungens K, Prospero S. Emergence of the sudden oak death pathogen Phytophthora ramorum. Trends in Microbiology. 2012 ;20:131-138.
  2. Goss EM, Tabima JF, Cooke DEL, Restrepo S, Fry WE, Forbes GA, Fieland VJ, Cardenas M, Grünwald NJ. The Irish potato famine pathogen Phytophthora infestans originated in central Mexico rather than the Andes. Proceedings of the National Academy of Sciences [Internet]. 2014 ;111(24):8791-8796 . Available from: http://www.pnas.org/content/early/2014/05/29/1401884111.abstract
  3. Goss EM, Larsen M, Chastagner GA, Givens DR, Grünwald NJ. Population Genetic Analysis Infers Migration Pathways of Phytophthora ramorum in US Nurseries. PLoS Pathogens. 2009 ;5.
  4. Kamvar ZN, Larsen MM, Kanaskie AM, Hansen EM, Grünwald NJ. Spatial and temporal analysis of populations of the sudden oak death pathogen in Oregon forests. Phytopathology [Internet]. 2015 :PHYTO-12-14-0350-FI. Available from: http://dx.doi.org/10.1094/PHYTO-12-14-0350-FI
  5. Grünwald NJ, Goss EM. Evolution and Population Genetics of Exotic and Re-Emerging Pathogens: Novel Tools and Approaches. Annual Review of Phytopathology. 2011 ;49:249-267.
  6. Knaus BJ, Tabima JF, Davis CE, Judelson HS, Grünwald NJ. Genomic Analyses of Dominant US Clonal Lineages of Phytophthora infestans Reveals a Shared Common Ancestry for Clonal Lineages US11 and US18 and a Lack of Recently Shared Ancestry Among All Other US Lineages. Phytopathology. 2016 :PHYTO–10.
  7. Grünwald NJ, McDonald BA, Milgroom MG. Population Genomics of Fungal and Oomycete Pathogens. Annual Review of Phytopathology [Internet]. 2016 ;54:323–46. Available from: http://dx.doi.org/10.1146/annurev-phyto-080614-115913
  8. Kamvar ZN, Tabima JF, Grünwald NJ. Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ [Internet]. 2014 ;2:e281. Available from: http://dx.doi.org/10.7717/peerj.281
  9. Kamvar ZN, Brooks JC, Grünwald NJ. Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality. Frontiers in Genetics [Internet]. 2015 ;6. Available from: http://www.frontiersin.org/plant_genetics_and_genomics/10.3389/fgene.2015.00208/abstract
  10. Knaus BJ, Grünwald NJ. vcfr: a package to manipulate and visualize variant call format data in R. Molecular Ecology Resources. 2017 ;17:44–53.
  11. Foster ZSL, Sharpton T, Grünwald NJ. MetacodeR: An R package for manipulation and heat tree visualization of community taxonomic data from metabarcoding. bioRxiv. 2016 :071019.
  12. Tabima JF, Everhart SE, Larsen MM, Weisberg AJ, Kamvar ZN, Tancos MA, Smart CD, Chang JH, Grünwald NJ. Microbe-ID: an open source toolbox for microbial genotyping and species identification. PeerJ [Internet]. 2016 ;4:e2279. Available from: https://doi.org/10.7717/peerj.2279
  13. Parke JL, Knaus BJ, Fieland VJ, Lewis C, Grünwald NJ. Phytophthora community structure analyses in Oregon nurseries inform systems approaches to disease management. Phytopathology. 2014 ;104(10):1052-62.
  14. Knaus BJ, Fieland VJ, Graham KA, Grünwald NJ. Diversity of Foliar Phytophthora Species on Rhododendron in Oregon Nurseries. PLANT DISEASE. 2015 ;99:1326-1332.
  15. Parke JL, Grünwald NJ. A Systems Approach for Management of Pests and Pathogens of Nursery Crops. Plant Disease. 2012 ;96:1236-1244.