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

Location: Foreign Disease-Weed Science Research

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

Genome evolution and transcriptome plasticity associated with adaptation to monocot and eudicot plants in Colletotrichum fungi Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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.