2012 Annual Report 1a.Objectives (from AD-416): Overall objective is to improve the existing Puccinia graminis draft genome sequence (strain 7a) and provide a complete web resource for the scientific community. The specific objectives are to: (a) improve the reference genome (b) comprehensively refine the annotation using RNA-sequencing (c) establish a genetic framework to resolve haplotypes, (d) provide a reference for the current epidemic rust strain, Ug99, and (e) provide a web-based information infrastructure for delivery of this information. 1b.Approach (from AD-416): Objectives 1 and 2 involve the improvement of the existing P. graminis reference genome, through the genetic linkage of existing supercontigs and the generation of novel RNA-seq data to support gene annotation. Objective 3 is to prototype a novel genetic approach to distinguish the two haplotypes of 7a, which if successful, will also lead to an improvement in the quality of the 7a reference. Objective 4 is to generate a de novo assembled reference sequence for the Ug99 strain and to annotate this genome (the improved annotation of the reference strain will assist in this process). Objective 5 is to use both these strains as reference sequence to integrate other high throughput data sets (specifically, with variation data from other strains of Pgt) and to disseminate this data to the scientific community in the context of other fungal genomic data, through Ensembl (a genome informatics portal maintained by the European Bioinformatics Institute) and the Broad Institute rust fungal genomes website. 3.Progress Report: This project is part of a larger program on the genomic analysis of the wheat stem rust fungus (Puccinia graminis f. sp. tritici) and development of genomic resources for the community of researchers working on wheat rust pathogens. Isolates of an F2 mapping population of P. graminis were increased, DNA extracted, and submitted for NexGen sequencing. RNA transcriptome experiment was planned, infected wheat materials generated, RNA extracted, and submitted for RNA sequencing.