Whole genome sequencing of the soil fungus Rhizoctonia solani anastomosis group 3
The fungus Rhizoctonia solani anastomosis group 3 (AG-3) is a common inhabitant of the soil ecosystem and has a worldwide distribution. R. solani is an economically important pathogen that affects food crops mostly in the plant family Solanaceae, including eggplant, pepper, potato and tomato. In addition to the ability of the fungus to cause plant disease, it can also grow as a saprobe on dead plant material to promote the recycling of organic matter. The research will provide a unique opportunity to examine the genome of a plant pathogen that represents an important early diverging and transitional group of the mushroom forming fungi in the Agaricomycotina.
We are currently conducting whole genome sequencing of R. solani AG-3 using Sanger, 454 and Illumina sequencing platforms. Normalized, full-length cDNAs generated during six different phases of fungal development and an optical map have been developed to aid in the assembly and annotation of the genome sequence. The strain being sequenced (Rhs1AP) is a heterokaryon with multinucleate hyphal cells that contains at least two genetically distinct nuclear genomes. To further assist in genome assembly, strains with a reduced genomic complement of strain Rhs1AP have been developed. Genomic DNA from one of these strains (Rhs1AP-123E) is currently being sequenced using the Illumina platform. The assembly from strain Rhs1AP-123E will assist in resolving the structure of the chromosomes associated with the genetically distinct nuclei of the heterokaryotic strain Rhs1AP. We will develop a comprehensive database for comparative and functional genomics experiments with additional members of the R. solani species complex to address issues related to fungal cell metabolism, developmental biology, ecology, and plant host specificity. The proposed research will provide insight into understanding the biochemical and molecular events regulating the parasitic and saprobic activity of R. solani such that new disease management strategies can be developed to increase agricultural productivity and sustainability.