Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions

Background: The pan-genome of a bacterial species consists of a core and an accessory gene pool. The accessory genome is thought to be an important source of genetic variability in bacterial populations and is gained through lateral gene transfer, allowing subpopulations of bacteria to better adapt to specific niches. Low-cost and highthroughput sequencing platforms have created an exponential increase in genome sequence data and an opportunity to study the pan-genomes of many bacterial species. In this study, we describe a new online pangenome sequence analysis program, Panseq. Results: Panseq was used to identify Escherichia coli O157:H7 and E. coli K-12 genomic islands. Within a population of 60 E. coli O157:H7 strains, the existence of 65 accessory genomic regions identified by Panseq analysis was confirmed by PCR. The accessory genome and binary presence/absence data, and core genome and single nucleotide polymorphisms (SNPs) of six L. monocytogenes strains were extracted with Pa...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Chad Laing, Cody Buchanan, Eduardo N. Taboada, Yongxiang Zhang, Andrew Kropinski, Andre Villegas, James E. Thomas, Victor P. J. Gannon
• Keywords: Accessory Genome, Accessory Genomic Regions, Bacterial Species, BMCBI 2010