Research Project: Integrative Genomic and Biological Approaches to Detect and Manage Emerging Foreign Fungal and Oomycete Plant Pathogens

Location: Foreign Disease-Weed Science Research

Publications (Clicking on the reprint icon will take you to the publication reprint.)

Intraspecies sequence-graph analysis of the Phytophthora theobromicola genome reveals a dynamic structure and variable effector repertoires - (Peer Reviewed Journal)
Garcia, J.F., Figueroa-Balderas, R., Puig, A.S., Baruah, I.K., Matson, M., Ali, S.S., Bailey, B.A., Marelli, J., Cantu, D. 2025. Intraspecies sequence-graph analysis of the Phytophthora theobromicola genome reveals a dynamic structure and variable effector repertoires. G3: Genes, Genomes, Genetics. https://doi.org/10.1101/2025.07.17.665439.

Evidence of graft incompatibility and rootstock scion interactions in cacao - (Peer Reviewed Journal)
Duval, A., Tempeleu, A., Schmidt, J., Puig, A.S., Knollenberg, B., Chaparro, J., Motamayor, J. 2025. Evidence of graft incompatibility and rootstock scion interactions in cacao. Horticulturae. https://doi.org/10.3390/horticulturae11080899.

Biological invasions: a global assessment of geographic distributions, long-term trends, and data gaps - (Peer Reviewed Journal)
Seebo, H., Meyerson, L., Richardson, D., Pyšek, P., Franck, C., Hui, C., Tricarico, E., Garcia-Diaz, P., Thines, M., Crouch, J. 2025. Biological invasions: a global assessment of geographic distributions, long-term trends, and data gaps. Biological Reviews. https://doi.org/10.1111/brv.70058.

New or unusual oomycetes collected from turfgrass in New Jersey and North Carolina. - (Abstract Only)

Behavior of rose downy mildew on leaves and flowers of a variety of plants in the Rosaceae - (Abstract Only)

The effects of sanitizers on Calonectria pseudonaviculata and C. henricotiae conidia and microsclerotia viability - (Peer Reviewed Journal)
Shishkoff, N., Lamondia, J.A., Cowles, R.S. 2025. The effects of sanitizers on Calonectria pseudonaviculata and C. henricotiae conidia and microsclerotia viability. Journal of Environmental Horticulture. 43(2):83–90. http://meridian.allenpress.com/jeh/article-pdf/43/2/83/3522793/i2573-5586-43-2-83.pd.

Analysis of the genetic diversity of the soybean rust pathogen Phakopsora pachyrhizi reveals two major evolutionary lineages - (Peer Reviewed Journal)
Rocha, V., Ferreira, E., Castanho, F., Kuwahara, M., Godoy, C., Meyer, M., Pedley, K.F., Voegele, R., Grigoriev, I., Lipzen, A., Barry, K., Loehrer, M., Schaffrath, U., Sirven, C., Duplessis, S., Guimarães, F. 2025. Analysis of the genetic diversity of the soybean rust pathogen Phakopsora pachyrhizi reveals two major evolutionary lineages. Fungal Genetics and Biology. 179. Article 103990. https://doi.org/10.1016/j.fgb.2025.103990.

Production of the light-activated elsinochrome phytotoxin in the soybean pathogen Coniothyrium glycines hints at virulence factor - (Peer Reviewed Journal)
Greatens, N., Murithi, H., Coyne, D., Clough, S.J., Sulyok, M., Okunowo, W., Abbas, H.K., Shier, W., Koch Bach, R.A. 2025. Production of the light-activated elsinochrome phytotoxin in the soybean pathogen Coniothyrium glycines hints at virulence factor. PLOS ONE. https://doi.org/10.1371/journal.pone.0321896.

Virulence and genotypic diversity of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici) detected in Jordan - (Peer Reviewed Journal)

A 2023-2024 literature review of validation standards and diagnostic accuracy - (Literature Review)
Nascimento, D.M., Sharma, P., Luster, D.G., Cardwell, K.F. 2025. A 2023-2024 literature review of validation standards and diagnostic accuracy. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-12-24-0132-FI.

Evaluation of wheat blast resistance in the USDA hard winter wheat (Triticum aestivum L.) Northern and Southern Regional Performance Nurseries - (Peer Reviewed Journal)
Pedley, K.F., Boehm Jr, J.D., Bai, G., St Amand, P.C., Peterson, G.L., Vinyard, B.T. 2025. Evaluation of wheat blast resistance in the USDA hard winter wheat (Triticum aestivum L.) Northern and Southern Regional Performance Nurseries. Plant Disease. https://doi.org/10.1094/PDIS-09-24-1941-RE.

The 2024 Outline of Fungi and fungus-like taxa - (Review Article)
Hyde, K.D., Noorabadi M.T,. Thiyagaraja V., He M.Q., Johnston P.R., Wijesinghe S.N., Armand A., Groenewald J.Z., Cai L., Crouch J.A., Crous P.W., Damm U., Zvyagina E. 2024 – The 2024 Outline of Fungi and fungus-like taxa. Mycosphere 15(1), 5146–6239. 

The Select Agent Coniothyrium glycines represents a species complex - (Peer Reviewed Journal)
Koch Bach, R.A., Murithi, H.M., Clough, S.J., Coyne, D. 2024. The Select Agent Coniothyrium glycines represents a species complex. Mycologia. https://doi.org/10.1080/00275514.2024.2383114.

Genome evolution and transcriptome plasticity associated with adaptation to monocot and eudicot plants in Colletotrichum fungi - (Peer Reviewed Journal)
Baroncelli, R., Cobo-Diaz, J.F., Benocci, T., Peng, M., Battaglia, E., Haridas, S., Andreopoulos, W., Labutti, K., Pangilinan, J., Lipzen, A., Koriabine, M., Bauer, D., Le Floch, G., Makela, M.R., Drula, E., Henrissat, B., Grigoriev, I.V., Crouch, J., De Vries, R.P., Sukno, S.A., Thon, M.R. 2024. Genome evolution and transcriptome plasticity associated with adaptation to monocot and eudicot plants in Colletotrichum fungi. Gigascience 13:1-18. https://doi.org/10.1093/gigascience/giae036.

Supporting data for: Genome evolution and transcriptome plasticity associated with adaptation to monocot and eudicot plants in Colletotrichum fungi - (Database / Dataset)
Baroncelli, R., Cobo-Díaz, J., Benocci, T., Peng, M., Battaglia, E., Haridas, S., Andreopoulos, W., Labutti, K., Pangilinan, J., Lipzen, A., Koriabine, M., Bauer, D., Le Floch, G., Mäkelä, M.R., Drula, E., Henrissat, B., Grigoriev, I., Crouch, J., De Vries, R., Sukno, S., Thon, M. 2024. Supporting data for: Genome evolution and transcriptome plasticity associated with adaptation to monocot and eudicot plants in Colletotrichum fungi. Gigascience. https://doi.org/10.5524/102528.

The soybean Rpp3 gene encodes a TIR-NBS-LRR protein that confers resistance to Phakopsora pachyrhizi - (Peer Reviewed Journal)
Bish, M.D., Ramachandran, S.R., Wright, A.L., Lincoln, L.M., Whitham, S.A., Graham, M.A., Pedley, K.F. 2024. The soybean Rpp3 gene encodes a TIR-NBS-LRR protein that confers resistance to Phakopsora pachyrhizi. Molecular Plant-Microbe Interactions. 37:561-570. https://doi.org/10.1094/MPMI-01-24-0007-R.

Remarkably high internal transcribed spacer haplotype diversity of the fungal select agent Coniothyrium glycines discovered throughout its range in Sub-Saharan Africa - (Peer Reviewed Journal)
Koch Bach, R.A., Murithi, H.M., Slocum, C.R., Coyne, D., Clough, S.J. 2024. Remarkably high internal transcribed spacer haplotype diversity of the fungal select agent Coniothyrium glycines discovered throughout its range in Sub-Saharan Africa. Phytopathology. https://doi.org/10.1094/PHYTO-09-23-0315-KC.

Rapid mini-chromosome divergence among fungal isolates causing wheat blast outbreaks in Bangladesh and Zambia - (Peer Reviewed Journal)
Liu, S., Lin, G., Ramachandran, S.R., Calderon Daza, L., Cruppe, G., Tembo, B., Singh, P., Cook, D., Pedley, K.F., Valent, B. 2023. Rapid mini-chromosome divergence among fungal isolates causing wheat blast outbreaks in Bangladesh and Zambia. New Phytologist. 241:1266-1276. https://doi.org/10.1111/nph.19402.

A soybean rust effector protease suppresses host immunity and cleaves a 3-deoxy-7-phosphoheptulonate synthase - (Pre-print Publication)
Sartor Chicowski, A., Qi, M., Montes, C., Variz, H., Caiazza, F., Bredow, M., Dong, H., Margets, A., Walley, J., Aung, K., Craik, C.S., Pedley, K.F., Innes, R., Whitham, S.A. 2023. A soybean rust effector protease suppresses host immunity and cleaves a 3-deoxy-7-phosphoheptulonate synthase. bioRxiv. https://doi.org/10.1101/2023.09.07.556260.

Boxwood phyllosphere fungal and bacterial communities and their differential responses to film-forming anti-desiccants - (Peer Reviewed Journal)
Li, X., Omolehin, O., Hemmings, G., Tseng, H., Taylor, A., Taylor, C., Daughtrey, M., Luster, D.G., Gouker, F.E., Hong, C. 2023. Boxwood phyllosphere fungal and bacterial communities and their differential responses to film-forming anti-desiccants. BMC Microbiology. https://doi.org/10.1186/s12866-023-02956-0.

A re-evaluation of phylogenomic data reveals that current understanding in wheat blast population biology and epidemiology is obfuscated by oversights in population sampling - (Peer Reviewed Journal)
Farman, M.L., Ascari, J.P., Rahnama, M., Del Ponte, E.M., Pedley, K.F., Martinez, S., Fernandes, J.C., Valent, B. 2023. A re-evaluation of phylogenomic data reveals that current understanding in wheat blast population biology and epidemiology is obfuscated by oversights in population sampling. Phytopathology. 114:220-225. https://doi.org/10.1094/PHYTO-01-23-0025-R.

A re-evaluation of phylogenomic data reveals that current understanding in wheat blast population biology and epidemiology is obfuscated by oversights in population sampling - (Pre-print Publication)
Farman, M.L., Ascari, J.P., Rahnama, M., Del Ponte, E.M., Pedley, K.F., Martinez, S., Fernandes, J.C., Valent, B. 2022. A re-evaluation of phylogenomic data reveals that current understanding in wheat blast population biology and epidemiology is obfuscated by oversights in population sampling. bioRxiv. https://doi.org/10.1101/2022.12.19.521104.

Evaluation of fungicides for management of boxwood blight caused by Calonectria spp. under field conditions in northern Germany - (Peer Reviewed Journal)
Brand, T., Beltz, H., Adhikari, U., Daughtrey, M., Luster, D.G., Kong, P., Hong, C. 2022. Evaluation of fungicides for management of boxwood blight caused by Calonectria spp. under field conditions in northern Germany. Journal of Plant Diseases and Protection. 130:325–335. https://doi.org/10.1007/s41348-022-00691-8.

Population genomics provide insights into the global genetic structure of Colletotrichum graminicola, the causal agent of maize anthracnose - (Peer Reviewed Journal)
Rogério, F., Baroncell, R., Cuevas-Fernández, F., Becerra, S., Crouch, J., Bettiol, W., Azcárate-Peril, A.M., Malapi-Wight, M., Ortega, V., Betran, J., Tenuta, A., Dambolena, J.S., Esker, P.D., Revilla, P. 2022. Population genomics provide insights into the global genetic structure of Colletotrichum graminicola, the causal agent of maize anthracnose. mBio. 14(1):02878-22. https://doi.org/10.1128/mbio.02878-22.

Genome sequence resources for five isolates of Coniothyrium glycines, causal pathogen of red leaf blotch of soybean - (Peer Reviewed Journal)
Proaño-Cuenca, F., Carrera-Lopez, D., Luster, D.G., Zeller, K., Cardwell, K.F. 2023. Genome sequence resources for five isolates of Coniothyrium glycines, causal pathogen of red leaf blotch of soybean. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-10-22-0113-A.

Genome evolution and transcriptome plasticity associated with adaptation to monocot and eudicot plants in Colletotrichum fungi - (Pre-print Publication)
Baroncelli, R., Cobo-Díaz, J., Benocci, T., Peng, M., Battaglia, E., Haridas, S., Andreopoulos, W., Labutti, K., Pangilinan, J., Lipzen, A., Koriabine, M., Bauer, D., Le Floch, G., Mäkelä, M.R., Drula, E., Henrissat, B., Grigoriev, I., Crouch, J., De Vries, R., Sukno, S., Thon, M. 2022. Genome evolution and transcriptome plasticity associated with adaptation to monocot and eudicot plants in Colletotrichum fungi. bioRxiv. 508453. https://doi.org/10.1101/2022.09.22.508453.

Rapid mini-chromosome divergence among fungal isolates causing wheat blast outbreaks in Bangladesh and Zambia - (Pre-print Publication)
Liu, S., Lin, G., Ramachandran, S.R., Cruppe, G., Cook, D.E., Pedley, K.F., Valent, B. 2022. Rapid mini-chromosome divergence among fungal isolates causing wheat blast outbreaks in Bangladesh and Zambia. bioRxiv. https://doi.org/10.1101/2022.06.18.496690.