| Article ID | Journal | Published Year | Pages | File Type |
|---|---|---|---|---|
| 2820582 | Genomics | 2015 | 6 Pages |
•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.
