Fig. 5

Pathogen genome comparisons reveal patient-specific additions. Two public reference genomes of S. maltophilia are compared against assembled contigs from patient CF-00. a Genome-wide alignment showing blocks of colinearity, additions, and deletions. White stretches indicate unalignable, unique regions in each genome. Vertical red lines separate individual assembled contigs. b Magnified view centered on a genomic region that is unique to the strain in patient CF-00. Genes with homology to type six secretion system (T6SS) have been labeled with numerical IDs (see panel c below). Genes marked with an asterisk showed no detectable homology in sequence databases. c The core gene cluster of T6SS is depicted in yellow; additional accessory T6SS genes which are also observed in patient CF-00 are colored in gray. d Schematic model of the T6SS protein structure based on present knowledge