bacLIFE

bacLIFE predicts lifestyle-associated genes and performs genome annotation and large-scale comparative genomics to identify genes linked to bacterial niche adaptation.

Key Features:

• Genome annotation: Integrates genome annotation for bacterial genomes to support downstream comparative analyses.
• Large-scale comparative genomics: Performs comparative genomics across extensive datasets to detect gene presence–absence patterns associated with lifestyles.
• Prediction of lifestyle-associated genes (LAGs): Identifies candidate genes associated with specific bacterial lifestyles and niche adaptation.
• High-throughput application: Applied at scale to 16,846 bacterial genomes from Burkholderia/Paraburkholderia and Pseudomonas.
• Identification of candidate gene families: Reported hundreds of genes linked to a plant pathogenic lifestyle, including glycosyltransferase, extracellular binding proteins, homoserine dehydrogenases, and hypothetical proteins.
• Experimental validation linkage: Predictions were subjected to experimental validation by site-directed mutagenesis and plant bioassays, confirming involvement of six genes in phytopathogenic lifestyles.

Scientific Applications:

• Discovery of LAGs: Detection of genes associated with plant pathogenicity and other niche-adaptive lifestyles.
• Bacterial-host interaction hypotheses: Generation of hypotheses about bacterial interactions with eukaryotic hosts based on predicted LAGs.
• Comparative studies across genera: Comparative analysis of Burkholderia/Paraburkholderia and Pseudomonas genomes to link genotypes to ecological niches.
• Experimental target selection: Prioritization of candidate genes for functional testing such as site-directed mutagenesis and plant bioassays.

Methodology:

Integrates genome annotation with large-scale comparative genomics to predict lifestyle-associated genes and was applied to 16,846 Burkholderia/Paraburkholderia and Pseudomonas genomes.