Acinetobacter baumannii GC1 recombination analysis

Analysis of recombination within the genomes of Acinetobacter baumannii Global Clone 1 (GC1). These data accompany the paper: Holt KE, Kenyon JJ, Hamidian M, Schultz MB, Pickard DJ, Dougan G, Hall RM. "Five decades of genome evolution in the globally distributed, extensively antibiotic resistant pathogen Acinetobacter baumannii GC1", Microbial Genomics, 2016. The files provided here are in the formats required for viewing in JScandy, available at http://jameshadfield.github.io/JScandy/. Simply drag and drop the GFF, CSV and tree files onto the browser window to view the data in interactive format. The reference genome for Acinetobacter baumannii GC1 strain A1 was sequenced using PacBio and Illumina Hiseq platforms, and is available in NCBI under accession NZ_CP010781.1 (provided here in GFF format, "A1.gff"). Additional genomes were sequenced using Illumina HiSeq (accessions for individual genome data are given in Supp Table 1) or sourced from public data sets (accessions for individual genome data are given in Supp Table 2). Recombination analysis was performed using Gubbins (available https://github.com/sanger-pathogens/gubbins), see Holt et al, MGen 2016 (in reference list) for details. Recombination blocks detected by Gubbins are in the file GubbinsOutput.gff. A maximum likelihood phylogeny for the GC1 genomes, which excludes these recombinant blocks and therefore captures the vertical inheritance relationships between the genomes, output by Gubbins is given in the newick-format tree file GC1.tree. This is the tree shown in Figure 1 of the paper. For strains with known isolation dates, BEAST (http://beast.bio.ed.ac.uk) was used to generate a dated phylogeny from the recombination-free alignment (file GC1_BEAST.tree); this is the tree shown in Figure 2 of the paper. Genotypes for the capsular synthesis (K) locus and the outer core polysaccharide (OC) locus were determined from the genome assemblies and are listed in K_OC.csv Screenshots from the visualisation of these files (ML tree only) using JScandy are ...