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Genomics. 2015 Dec;106(6):367-72. doi: 10.1016/j.ygeno.2015.10.001. Epub 2015 Oct 9.

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

Author information

1
Department of Microbiology, University of Washington, Seattle, WA 98195 USA. Electronic address: sandipp@u.washington.edu.
2
CSIR - National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India. Electronic address: archana2287@gmail.com.
3
CSIR - National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India. Electronic address: sumit.bag@nbri.res.in.
4
Department of Microbiology, University of Washington, Seattle, WA 98195 USA. Electronic address: evs@u.washington.edu.
5
Department of Microbiology, University of Washington, Seattle, WA 98195 USA. Electronic address: sujayc@u.washington.edu.

Abstract

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.

KEYWORDS:

Core-genome; Draft-genome annotation; Pan-genome; Protein-coding genes

PMID:
26456591
PMCID:
PMC4811333
DOI:
10.1016/j.ygeno.2015.10.001
[Indexed for MEDLINE]
Free PMC Article

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