PanCoreGen — Profiling, detecting, annotating protein-coding genes in microbial genomes

• PanCoreGen is a standalone tool for pan-/core-genomic profiling of microbial protein-coding genes.
• It can annotate draft genomes/contigs, detect unidentified genes in annotated genomes, and perform user-defined group-specific analysis for pan-genomic profiling.
• It allows analysis of both user-provided draft genomes and publicly available annotated and draft genomes in GenBank.
• Output gene sequence datasets can readily be used for further applications in population genomics, phylogenomics and pathogenomics study.
• The results of a test dataset of Salmonella enterica genomes suggested footprints of adaptive convergence of horizontally transferred genes.

A large amount of genomic data, especially from multiple isolates of a single species, has opened new vistas for microbial genomics analysis. Analyzing the pan-genome (i.e. the sum of genetic repertoire) of microbial species is crucial in understanding the dynamics of molecular evolution, where virulence evolution is of major interest. Here we present PanCoreGen — a standalone application for pan- and core-genomic profiling of microbial protein-coding genes. PanCoreGen overcomes key limitations of the existing pan-genomic analysis tools, and develops an integrated annotation-structure for a species-specific pan-genomic profile. It provides important new features for annotating draft genomes/contigs and detecting unidentified genes in annotated genomes. It also generates user-defined group-specific datasets within the pan-genome. Interestingly, analyzing an example-set of Salmonella genomes, we detect potential footprints of adaptive convergence of horizontally transferred genes in two human-restricted pathogenic serovars — Typhi and Paratyphi A. Overall, PanCoreGen represents a state-of-the-art tool for microbial phylogenomics and pathogenomics study.