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Development of Tools, Models and Datasets For Genome-enabled Studies of Bacterial Phytopathogens

Investigators
Stodghill P
Institutions
USDA - Agricultural Research Service
Start date
2017
End date
2022
Objective
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.
Funding Source
Agricultural Research Service
Project source
View this project
Project number
8062-22000-043-00D
Accession number
432869
Categories
Prevention and Control
Commodities
Nuts, Seeds