Gall-ID

Gall-ID provides genotyping and identification of gall-forming phytopathogenic bacteria (including Agrobacterium, Pseudomonas savastanoi, Pantoea agglomerans, and Rhodococcus) using 16S rDNA, multilocus sequence analysis (MLSA), whole-genome sequences, and high-throughput sequencing to classify taxa and detect virulence gene homologs.

Key Features:

• Taxonomic Classification: Uses 16S rDNA, multilocus sequence analysis (MLSA), and whole-genome sequence data to classify gall-associated bacteria at high resolution.
• High-Throughput Sequencing Integration: Analyzes high-throughput sequencing reads to search for homologs of characterized virulence genes.
• Automated Software Pipelines: Provides software pipelines that automate MLSA, compute average nucleotide identity (ANI), and construct core genome phylogenies.
• Comprehensive Databases: Includes databases for identifying additional plant-pathogenic bacteria within microbial communities associated with galls or diseased plant tissues.

Scientific Applications:

• Population genetics: Analyzes population structure and genetic diversity of gall-associated plant pathogens.
• Pathogen evolution: Assesses how agricultural practices may influence pathogen evolution through comparative genomic analyses.
• Disease management: Informs development of targeted disease management strategies via taxonomic resolution and virulence gene detection.
• Host–pathogen studies: Supports elucidation of interactions between phytopathogenic bacteria and their plant hosts.

Methodology:

Performs sequence-based analyses using 16S rDNA, MLSA, and whole-genome sequences; analyzes high-throughput sequencing reads for virulence gene homologs; and executes pipelines for MLSA automation, average nucleotide identity (ANI) calculation, and core genome phylogeny construction.