Jonathan Richards

Plants have developed an innate immune system, consisting of molecules that act in surveillance and perception of their environment. Host recognition of pathogenic fungi triggers a robust defense response which typically restricts further pathogen growth or reproduction. To overcome this defense, plant pathogenic fungi have co-evolved effector molecules (including proteins, secondary metabolites, and small RNA molecules) to evade or suppress the plant immune system. Broadly, my research aims to understand the molecular events occurring in both host and pathogen during compatible or incompatible interactions, as well as understand the fungal genomic and evolutionary forces that lead to virulence/avirulence.

My lab focuses on i) characterizing molecular mechanisms involved in fungal pathogenesis and virulence, ii) understanding fungal genome evolution and population biology, and iii) elucidating the molecular components and spatiotemporal dynamics of the host defense response. In nearly all facets of our research, we strive to leverage next-generation sequencing methods combined with classical genetics and molecular biology techniques to dissect these complex interactions. We primarily use the rice – Cercospora janseana (narrow brown leaf spot) and soybean – Cercospora sojina (frogeye leaf spot) pathosystems as experimental systems to investigate host-pathogen interactions with an emphasis on fungal effectors, biology of the hemibiotrophic lifestyle, and tissue-specific host resistance mechanisms. Additionally, as Cercospora spp. are highly relevant in agricultural and ecological settings, our genome structure and evolution research focuses on gene family expansion/contraction, transposable element content, and structural variation encompassing the breadth of this genus.

Searight, J., Famoso, A.N., Zhou, X., Doyle, V.P., and Richards, J.K. 2023. A high-quality genome assembly for Cercospora janseana, causal agent of narrow brown leaf spot of rice. Molecular Plant-Microbe Interactions. DOI: 10.1094/MPMI-10-22-0222-A 

Richards, J.K., Li, J., Koladia, V., Wyatt, N.A., Rehman, S., Brueggeman, R.S., and Friesen, T.L. 2023. A Moroccan Pyrenophora teres f. teres population defeats the Rpt5 broad-spectrum resistance on barley chromosome 6H. Phytopathology. DOI: 10.1094/PHYTO-04-23-0117-R

Khan, A., David, R.B., Richards, J., Bansal, U., Wang, C., McCartney, C., Stam, R., and Wang, N. 2023. Plant disease resistance research at the dawn of a new era. Phytopathology. 113:756-759. DOI: 10.1094/PHYTO-03-23-0108-FI 

Richards, J.K., Kariyawasam, G., Seneviratne, S., Wyatt, N.A., Xu, S.S., Liu, Z., Faris, J.D., and Friesen, T.L. 2022. A triple threat: the Parastagonospora nodorum SnTox267 effector exploits three distinct host genetic factors to cause disease in wheat. New Phytologist. 233:427-442. DOI: 10.1111/nph.17601

Kariyawasam, G.K., Richards, J.K., Wyatt, N.A., Running, K., Xu, S.S., Liu, Z., Borowicz, P., Faris, J.D., and Friesen, T.L. 2022. The Parastagonospora nodorum necrotrophic effector SnTox5 targets the wheat gene Snn5 and facilitates entry into the leaf mesophyll. New Phytologist. 233:409-426. DOI: 10.1111/nph.17602 

Clare, S.J., Duellman, K.M., Richards, J.K., Poudel, R.S., Merrick, L.F., Friesen, T.L., and Brueggeman, R.S. 2022. Association mapping reveals a reciprocal virulence/avirulence locus within diverse US Pyrenophora teres f. maculata isolates. BMC Genomics. 23:1-17. DOI: 10.1186/s12864-022-08529-1 

Ameen, G., Solanki, S., Sager-Bitarra, L,. Richards, J., Tamang, P., Friesen, T.L., and Brueggeman, R.S. 2021. Mutations in a barley cytochrome P450 gene enhances pathogen induced programmed cell death and cutin layer instability. PLoS Genetics. 17(12):e1009473 

Spanner, R., Taliadoros, D., Richards, J., Rivera-Varas, V., Neubauer, J., Natwick, M., Hamilton, O., Vaghefi, N., Pethybridge, S., Secor, G.A., Friesen, T.L., Stukenbrock, E.H., and Bolton, M.D. 2021. Genome-wide association studies reveal the complex genetic architecture of DMI fungicide resistance in Cercospora beticola. Genome Biology and Evolution. DOI: 10.1093/gbe/evab209 

Addison, C.K., Angira, B., Cerioli, T., Groth, D.E., Richards, J.K., Linscombe, S.D., and Famoso, A.N. 2021. Identification and mapping of a novel resistance gene to the rice pathogen, Cercospora janseana. Theoretical and Applied Genetics. 134: 2221-2234. DOI: 10.1007/s00122-021-03821-2 

Tamang, P., Richards, J.K., Solanki, S., Ameen, G., Sharma Poudel, R., Deka, P., Effertz, K., Clare, S., Hegstad, J., Bezbaruah, A.N., Li, X., Horsley, R.D., Friesen, T.L. and Brueggeman, R.S. 2021. The barley HvWRKY6 transcription factor is required for resistance against Pyrenophora teres f. teres. Frontiers in Genetics. 11:601500. DOI: 10.3389/fgene.2020.601500 

Richards, J.K., Xiao, C., and Jurick II, W.M. 2021. Botrytis spp.: a contemporary perspective and synthesis of recent scientific developments of a widespread genus that threatens global food security. Phytopathology. 111:432-436. DOI: 10.1094/PHYTO-10-20-0475-IA 

Wyatt, N.A., Richards, J.K., Brueggeman, R.S., and Friesen, T.L. 2020. A comparative genomic analysis of the barley pathogen Pyrenophora teres f. teres identifies subtelomeric regions as drivers of virulence. Molecular Plant Microbe Interactions. 33(2):173-188. DOI: 10.1094/MPMI-05-19-0128-R 

Aoun, M., Kolmer, J.A., Breiland, M., Richards, J., Brueggeman, R.S., Szabo, L.J., and Acevedo, M. 2020. Genotyping-by-sequencing for the study of genetic diversity in Puccinia triticina. Plant Disease. 104(3):752-760. DOI: 10.1094/PDIS-09-19-1890-RE 

Sharma Poudel, R., Richards, J., Shrestha, S., Solanki, S., and Brueggeman, R. 2019. Transcriptome-wide association study identifies putative elicitors/suppressor of Puccinia graminis f. sp. tritici that modulate barley rpg4-mediated stem rust resistance. BMC Genomics. 20:985. DOI: 10.1186/s12864-019-6369-7 

Richards, J. K., Stukenbrock, E., Carpenter, J., Liu, Z., Cowger, C., Faris, J., and Friesen, T.L. 2019. Local adaptation drives the diversification of effectors in the fungal wheat pathogen Parastagonospora nodorum in the United States. PLoS Genetics 15(10):e1008223. DOI: 10.1371/journal.pgen.1008223 (Journal Impact Factor: 6.020)