Objective 1: Develop datasets and computational tools to facilitate the study of large-scale genomic and pan-genomic features of plant-associated bacteria, including genomic islands and virulence pathways. [NP303, C2, PS2A] Subobjective 1A: Develop deep proteogenomic data sets to guide the annotation of poorly characterized type strains and field isolates of select strains of bacterial plant pathogens and other plant-associated bacteria. Subobjective 1B: Develop or refine annotation methods for genomic regions of anomalous nucleotide composition and the systems-level analysis of pathways related to virulence and adaptation to plant-associated niches. Objective 2: Identify genes and candidate transcription factor binding sites using comparative genomics and available CHIP-Seq, RNA-Seq and proteomics data sets, and ensure that gene calls include experimental evidence whenever appropriate. [NP303, C2, PS2A] Subobjective 2A: Extend comparative genomics methods to propagate the experimentally-supported genome annotate updates from targeted bacterial strains to related strains. Subobjective 2B: Leverage proteomics and other high-throughput datasets, along with comparative genomics methods, to identify conserved motifs representing candidate promoters and other regulatory binding sites.