General and contact information
Howard Judelson's background
education and interests
learn more about these exciting organisms
The late blight disease
learn more about the problems that P. infestans causes
Ongoing research projects
Other lab members
Opportunities for graduate study in the lab
Genomics of P. infestans
We were part of the project that used the traditional Sanger sequencing method to sequence the genome of P. infestans. Since then, we have made a major effort to improve both the genome assembly and its annotation. Using "next-generation" sequencing technologies including the Illumina and PacBio methods, we have recently generated a dramatically improved assembly in which the number of contigs was reduced, and assembly errors were corrected. Linkage analysis using SNPs has reduced the genome to 14 pseudochromosomes. Now, we are turning our attention to a better understanding of genome evolution and genome architecture, using modern bioinformatic tools.
The completed assembly: 14 pseudochromosomes
Size distribution of PacBio reads
Understanding the evolution of genes is an central objective of our work. 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 transcription factor binding site.
Visit our publications on this and other topics here.