A collaborative research project is currently being conducted to obtain a high quality complete genome sequence of the soil fungus Rhizoctonia solani anastomosis group 3 (AG-3) strain Rhs 1AP. This research project is being coordinated by William Nierman (J. Craig Venter Institute, Rockville, Maryland), Marc A. Cubeta and Ralph A. Dean (North Carolina State University) with funding from the United States Department of Agriculture Cooperative Research Education and Extension Service (USDA/CSREES) Microbial Genome Sequencing Program. A consortium of scientists in the Rhizoctonia community from Asia, Australia, Europe, and the Americas has been established to provide additional input on the project.

The Organism
The fungus Rhizoctonia solani anastomosis group 3 (AG-3) is a common inhabitant of the soil ecosystem, has a worldwide distribution, and represents the most genetically tractable member of the R. solani species complex The fungus is a pathogen of agricultural crops in the plant family Solanaceae that includes eggplant, pepper, potato, and tomato. In addition to its parasitic lifestyle, the fungus can also grow as a saprobe on non-living plant material to promote the decay and recycling of organic matter.

The complete DNA sequence of the fungus will reveal genes associated with its ability to cause plant disease and complement current genome sequencing projects on potato and tomato to increase our understanding of host parasite interactions. This information will lead to better ways of managing Rhizoctonia diseases that reduce economic loses to farmers and promote increased agricultural productivity and sustainability. In addition to understanding the genetic basis of phenotypic traits of economic and ecological importance, R. solani AG-3 represents an important evolutionary link to both beneficial and disease causing fungi.

Experimental Approach
A combination of Sanger ABI 3730xl and 454 Biosciences GS-FLX sequencing will be used. Sanger sequencing will involve a multiple shotgun library strategy with different insert sizes (e.g., 4 and 10 kb plasmid, and 40 kb fosmid) to obtain 6X sequence coverage and linkage of contigs, followed by assembly and annotation. This will be used in conjunction with one GS-FLX run to provide additional 10X coverage of the genome. Genome assembly will be validated by use of an optical restriction map. Sequencing of full-length and assembly of normalized cDNAs will be employed to augment annotation and provide authentic gene models to the annotation process. cDNA and EST libraries will also be used to analyze alternatively spliced isoforms and single nucleotide polymorphisms.

An educational outreach program will be developed for underrepresented groups of high school biology teachers and students from rural areas of eastern North Carolina. This program will focus on the use of genomics and bioinformatics related techniques to examine archaeological specimens of potato and R. solani.