Agricultural Microbes Genome 2 Conference

Poster: Microbial Genome Sequencing/Programs
P01_03.html

CONSTRUCTION OF A PHYSICAL AND TRANSCRIPTIONAL MAP OF THE PHYTOPHTHORA SOJAE GENOME

¹ Department of Plant Pathology, University of California, Davis, CA95616

² Department of Plant Pathology, University of California, Riverside CA 92521

³ Fungal Genomics Laboratory, NC State University, Raleigh, NC 27695-7251

⁴ National Center for Genome Resources,2935 Rodeo Park Drive East, Santa Fe, New Mexico 87505

⁵ Agriculture Canada, London Research Centre, London, Ontario N5V 4T3, Canada

The more than 40 species of the oomycete Phytophthora cause serious diseases of a huge range of crop and ornamental plants. To facilitate isolation of such genes from the soybean pathogen Phytophthora sojae by map-based cloning, we are constructing a BAC contig of the entire genome of this organism, using a hybridization fingerprinting strategy. We are hybridizing a 13X BAC library with unique mixtures of random probes, most of them repetitive, and with ESTs. Computer software has been developed to collect, simulate and analyze the data. At present we have probed the library with 49 of the mixtures. Each mixture hybridized to around 300 - 500 BACs. 19% of the BACs so far have received the minimum number of hits needed to establish statistically significant overlaps (5 each). Of these BACs, 34% have been placed into contigs. We have confirmed the authenticity of three of the largest contigs by HindIII digestion. With the long term goal of sequencing the entire genome of P. sojae and selected sequences from other Phytophthora species, such as P. infestans we have established the Phytophthora genome initiative (PGI). We have begun preliminary sequencing of a 200 kb BAC contig spanning two avirulence genes from P. sojae. Sequencing of the first 60 kb BAC is nearly complete, and software has been developed for automatic processing, annotation and publishing of the sequence data via the web. In the region sequenced so far the gene density is extremely high. Both the sequencing data and the BAC hybridization data suggest that the P.sojae genome is composed of gene-rich regions separated by regions rich in repetitive sequences.