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| Home page General and contact information Howard Judelson's background education and interests The oomycetes learn more about these exciting organisms The late blight disease learn more about the problems that P. infestans causes Research Interests Ongoing research projects Other lab members Publications Opportunities for graduate study in the lab |
Genomics of P. infestansThrough a collaboration between our lab, other labs in the Phytophthora community, and the Broad Institute of MIT and Harvard, the genome of P. infestans was sequenced with funding from the USDA/NSF Microbial Genome program. Needless to say, this data will accelerate all of our studies on this important organism. In particular, it will help us identify genes involved in growth and development, to understand how the P. infestans genome has evolved, to identify transcriptional regulatory signals, and to understand the evolution of the genus Phytophthora.
Our laboratory's major contribution to the project was to help refine the gene-calling process. Over 2000 genes were inspected an annotated manually by our laboratory.  The Argo system for viewing and improving gene models. This software interfaces with the database at the Broad Institute.  Genome assembly statistics (from our 2009 paper in Nature) Aiding in genome annotation was a large dataset of ESTs from P. infestans . We had constructed cDNA libraries representing multiple life-stages and growth conditions, which were sequenced by Syngenta and at NCSU. In total, about 105,000 ESTs were obtained. Prior to the completion of the P. infestans genome, the EST data was used to construct a Affymetrix GeneChip which we used to expression-profile the different stages of growth and development, both in P. infestans and the closely related species P. phaseoli.
(right) XY scatterplot analysis of P. infestans genes expressed during different stages of the asexual cycle. Major conclusions from the projects performed to date include the observation that P. infestans has a large and complex genome, with about 18,000 protein-coding genes and significant amounts of repeated DNA. The latter include both large families of retroelement-like sequences, and secreted proteins which may play role in infection by modulating the biology of host plants. Understanding the evolution and functions of the genes, both within P. infestans and between different Phytophthora species, is an central objective of our work. Some of these analyses involve detailed phylogenetic analyses of specific genes, such as a mating-associated gene illustrated in the tree shown below. This protein has evolved rapidly within the genus, and is believed to be a factor driving speciation.  Phylogenetic tree showing relationships between members of a multigene family within Phytophthora. The main tree is the M96 family, which encodes a surface glycoprotein found on the oospore. For comparison, relationships between selected species based on rDNA sequences are shown in the grey box. In other cases, we analyse whole families of proteins. For example, illustrated below is a phylogram of the protein kinases from P. infestans. There are about 350 such proteins made by the organism, which regulate various cellular processes by regulating the phosphorylation state of a range of other enzymes, ion channels, structural proteins, and others.  The protein kinases of P. infestans. We are also involved in promoter bioinformatics. The goal here is to identify regulatory motifs (transcription factor binding sites) that may be important in growth and development. Algorithms are being used that identify binding sites for stage-specific and general transcription factors (TFs) by searching for over-represented motifs within co-expressed genes, and testing for evolutionary conservation.  DNA motifs identified from P. infestans promoter subset.  Computational pipeline for motif-finding.  Graphical representation of a motif. Back to top
Research areas Home page and contact info Publications Graduate Studies updated 12.31.09
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