Department of Plant Plathology and Microbiology @ UCR

Our research seeks to characterize the genetics and developmental biology of oomycete fungi such as Phytophthora infestans, a species that causes the late blight diseases of tomato and potato. In the long term, our work will lead to a greater understanding of oomycete fungi and strategies for controlling them.

Most of our research involves characterizing genes involved in important aspects of the growth of P. infestans, particularly concerning the development and germination of spores. This is being pursued using the tools of genetics, genomics, proteomics, cell biology, and biochemistry. One part of the life cycle that interests us is the sexual cycle, which is important because it generates durable overwintering structures and strains with new pathogenic characteristics. Our studies of the sexual cycle have involved characterizing the loci that determine compatibility between isolates, and identifying genes required for the differentiation of the sexual spores. Asexual spore development is another aspect of the life cycle of P. infestans that we study, since such propagules play a key role in initiating infections of plants. This has involved identifying genes required for sporulation and germination, and identifying transcription factors required for development. Another area of Phytophthora biology that is being studied concerns fungicide resistance, which has frustrated growers' ability to control oomycete diseases in the field; genetic and biochemical approaches are being used to identify the basis of several forms of resistance that P. infestans shows to various fungicides.

Other areas of work involve the development of resources and tools for studying Phytophthora and related oomycetes. For example, to enable the analysis and manipulation of genes in oomycetes, we pioneered the development of gene transfer methods. We continue to advance and improve these techniques, for example by optimizing gene silencing methods and characterizing the nature of small RNAs (siRNAs) and the heterochromatin-modifying machinery that are involved in silencing.

We are also involved in the sequencing and analysis of the P. infestans genome, in collaboration with the Broad Institute of MIT and Harvard. Along these lines, bioinformatics has become a major part of many of our projects. For example, computational analyses are being used to identify promoter motifs, characterize transcriptional networks, and study the evolution of gene families. We are also a participant in the genome projects of other oomycetes, such as the downy mildew Hyaloperonospora parasitica.

Please visit the Judelson lab website at oomyceteworld.net. There is much more information there about our lab!

Haas, B., Kamoun, S., Zody, M., J, R., Handsaker, R.A., Cano, L., J. I. B. Bos, Broad Institute Genome Sequencing Platform, , M. Grabherr, C. D. Kodira, S. Raffaele, T. Torto-Alalibo, T. O. Bozkurt, A. M. V. Ah-Fong, L. Alvarado, V. L. Anderson, M. R. Armstrong, A. Avrova, L. Baxter, J. Beynon, P. C. Boevink, S. R. Bollmann, , V. Bulone, G. Cai, C. Cakir, J. C. Carrington, M. Chawner, L. Conti, S. Costanzo, R. Ewan, N. Fahlgren, M. A. Fischbach , J. Fugelstad,, E. M. Gilroy, S. Gnerre, P. J. Green, L. J. Grenville-Briggs, J. Griffith, N. J. Grünwald, K. Horn, N. R. Horner, C. Hu, E. Huitema, D. Jeong, A. M. E. Jones,, J. D. G. Jones, R. W. Jones, E. K. Karlsson, S. G. Kunjeti, K. Lamour, Z. Liu, L. Ma, D. MacLean, C. Marcus, H. McDonald, J. McWalters, H. J.G. Meijer, W. Morgan, P. F. Morris, C. A. Munro, K. O’Neill,, M. Ospina-Giraldo, A. Pinzón, L. Pritchard, B. Ramsahoye, Q. Ren, S. Restrepo, S. Roy, A. Sadanandom, A. Savidor, S. Schornack, D. C. Schwartz, U. D. Schumann, B. Schwessinger, L. Seyer,, T. Sharpe, C. Silvar, J. Song, D. J. Studholme, S. Sykes, M. Thines,, P. J. I. van de Vondervoort, P. Vipaporn, S. Wawra, R. Weide, J. Win, , C. Young, S. Zhou, W. Fry, B. C. Meyers, P. van West, J. Ristaino, F. Govers, P. R. J. Birch, S. C. Whisson, , Judelson, H.S., Nusbaum, C. Genome sequence and comparative analysis of the Irish potato famine pathogen Phytophthora infestans. 2009. Nature: in press.

Judelson, H.S., Narayan, R., Tani, S. 2009. Metabolic adaptation of Phytophthora infestans during growth on leaves, tubers, and artificial media. Molecular Plant Pathology 10: in press.

Xiang, Q., Roy, S., Kim, K., Judelson, H.S. 2009. A motif within a complex promoter from the oomycete Phytophthora infestansdetermines transcription during an intermediate stage of sporulation . Fungal Genetics and Biology 46: p.400-409.

Judelson, H. S., Narayan, R. D., Ah-Fong, A. M. V., and Kim, K-S. 2009. Gene expression changes during asexual sporulation by the late blight agent Phytophthora infestans occur in discrete temporal stages. Molecular Genetics and Genomics, 281, 193-206.

Ah-Fong, A. M. V., Bormann-Chung, C. A. and Judelson, H. S. 2008. Optimization of transgene-mediated silencing in Phytophthora infestans and its association with small interfering RNAs. Fungal Genetics and Biology 45, 1197-1205.

Ah-Fong, A. M. V., and Judelson, H. S. 2008. Molecular Strategies for Identifying Determinants of Oomycete Pathogenicity. Pages 383 to 410 in: Molecular Mechanisms of Plant and Microbe Coexistence (Nautiyal, C., and Dion, P. eds). Springer, Heidelberg.

H. S. Judelson, A. M. V. Ah-Fong, G. Aux, A. O. Avrova, C. Bruce, C. Cakir, L. da Cunha, L. Grenville-Briggs, M. Latijnhouwers, W. Ligterink, H. J.G. Meijer, S. Roberts, C. S. Thurber, S. C. Whisson, P. R. J. Birch, F. Govers, S. Kamoun, P. van West, and J. Windass. 2007. Gene expression profiling during asexual development of the late blight pathogen Phytophthora infestans reveals a highly dynamic transcriptome. Molecular Plant-Microbe Interactions 21, 433-447.

Ah-Fong, A. M.V., Xiang, Q., and Judelson, H. S. 2007. Architecture of the sporulation-specific Cdc14 promoter from the oomycete Phytophthora infestans. Eukaryotic Cell 6, 2222–2230.

Judelson, H. S. 2007. Sexual reproduction in plant pathogenic oomycetes: biology and impact on disease. Pages 445 to 458 In: Sex in fungi: molecular determination and evolutionary implications (J. Heitman, J. Kronstad, J. Taylor, L. Casselton, eds.). ASM Press, Washington DC.

Judelson, H. S., and Tani, S. 2007. Transgene-induced silencing of the zoosporogenesis-specific PiNIFC gene cluster of Phytophthora infestans involves chromatin alterations. Eukaryotic Cell 6, 1200-1209.

Judelson, H. S., Narayan, R., Ah Fong, A. M. V., Tani, S., and Kim, K. S. 2007. Performance of a tetracycline-responsive transactivator system for manipulating gene expression in the oomycete Phytophthora infestans. Current Genetics 51, 297-307.

Prakob, W. and Judelson, H. S. 2007. Gene expression during oosporogenesis in heterothallic and homothallic Phytophthora. Fungal Genetics and Biology 44, 726-739.

Judelson, H. S. 2007. Genomics of the plant pathogenic oomycete Phytophthora: insights into biology and evolution. Advances in Genetics 57, 98-142.

Judelson, H. S., and Ah Fong, A. M. V. 2007. Genomics of oomycetes. Pages 1 to 4 in: Encyclopedia of Plant and Crop Science (R. Goodman, ed.), Taylor and Francis, New York.

Judelson, H. S., and Senthil, G. 2006. Investigating the role of ABC transporters in multifungicide insensitivity in Phytophthora infestans. Molecular Plant Pathology 7, 17-29.

Cvitanich, C., Salcido, M., and Judelson, H. S. 2006. Concerted evolution of a tandemly arrayed family of mating-specific genes in Phytophthora analyzed through interspecific and intraspecific comparisons. Molecular Genetics and Genomics 275, 169-184.

Tani, S., and Judelson, H. S. 2006. Activation of zoosporogenesis-specific genes in Phytophthora infestans involves a seven-nucleotide promoter motif and cold-induced membrane rigidity. Eukaryotic Cell 42, 745-752.

Blanco, F.A., and H.S. Judelson. 2005. A bZIP transcription factor from Phytophthora interacts with a protein kinase and is required for zoospore motility and plant infection. Molecular Microbiology 56, 638-648.

Randall, T. A., Dwyer, R. A., Huitema, E., Beyer, K., Cvitanich, C., Kelkar, H., Ah Fong, A. M. V., Gates, K., Roberts, S., Yatzkan, E., Gaffney, T., Law, M., Testa, A., Torto, T. , Zhang, M., Zheng, L., Mueller, E., Windass, J., Binder, A. , Birch, P. R. J., Gisi, U., Govers, F., Gow, N. A., Mauch, F., van West, P., Waugh, M., Yu, J., Boller, T., Kamoun, S., Lam, S. T., and Judelson, H. S. 2005. Large-scale gene discovery in the oomycete Phytophthora infestans reveals likely components of phytopathogenicity shared with true fungi. Molecular Plant-Microbe Interactions 18:229-243

Tani, S., Kim, K.-S., and Judelson, H. S. 2005. A cluster of NIF transcriptional regulators with divergent patterns of spore-specific expression in Phytophthora infestans. Fungal Genetics and Biology 42, 42-50.

Judelson, H. S. and Blanco, F. A. 2005. The spores of Phytophthora: weapons of the plant destroyer. Nature Reviews Microbiology, 3:47-58

Ah Fong, A., and Judelson, H. S. 2004. The hAT-like DNA transposon, DodoPi, resides in a cluster of retro- and DNA transposons in the stramenopile Phytophthora infestans. Molecular Genetics and Genomics 271, 577-585.

Tani, S., Yatzkan, E., and Judelson, H. S. 2004. Multiple pathways regulate the induction of genes during zoosporogenesis in Phytophthora infestans. Molecular Plant Microbe Interactions 17, 330-337.

Kim, K., and Judelson, H. S. 2003. Sporangia-specific gene expression in the oomycete phytopathogen Phytophthora infestans. Eukaryotic Cell 2, 1376-1385.

Ah Fong, A., and Judelson, H. S. 2003. Cell cycle regulator Cdc14 is expressed during sporulation but not hyphal growth in the fungus-like oomycete Phytophthora infestans. Molecular Microbiology 50, 487-494.

Fabritius, A.-L. and Judelson, H. S. 2003. A mating-induced protein of Phytophthora infestans is a member of a family of elicitors with divergent structures and stage-specific patterns of expression. Molecular Plant-Microbe Interactions 16, 926-935.

Cvitanich, C. and Judelson, H. S. 2003. A gene expressed during sexual and asexual sporulation in Phytophthora infestans is a member of the Puf family of translational regulators. Eukaryotic Cell 2, 465-473.

Cvitanich, C. and Judelson, H. S. 2003. Transformation of the oomycete, Phytophthora infestans, using microprojectile bombardment. Current Genetics 42, 228-235.

Judelson, H. S. 2002. Sequence variation and genomic amplification of a family of Gypsy-like sequences in the oomycete genus Phytophthora. Molecular Biology and Evolution 19, 1313-1322.

Judelson, H. S. and S. Roberts. 2002. Novel protein kinase induced during sporangial cleavage in the oomycete Phytophthora infestans. Eukaryotic Cell 1, 687-695.

Fabritius, A.-L., and Judelson, H. S. 2002. Stage-specific gene expression during mating in Phytophthora infestans. Molecular Microbiology 45, 1057-1066.

Randall, T. A., Ah Fong, A., and Judelson, H. S. 2002. Chromosomal heteromorphism and an apparent translocation detected using a BAC contig spanning the mating type locus of Phytophthora infestans. Fungal Genetics and Biology 38, 75-84.

Judelson, H. S., and Tooley, P. W. 2000. Enhanced PCR methods for detecting and quantifying Phytophthora infestans in plants. Phytopathology 90, 1112-1119.

Judelson, H. S., and Fabritius, A-L. 2000. A linear RNA replicon from the oomycete, Phytophthora infestans. Molecular and General Genetics 263, 395-403.