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Analyses of Lateral Gene Transfer Events in Bacteroidetes Lineages Reveal Its Contribution to Niche Specialization

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posted on 19.06.2007, 02:28 by Jian Xu, Michael A Mahowald, Ruth E Ley, Catherine A Lozupone, Micah Hamady, Eric C Martens, Bernard Henrissat, Pedro M Coutinho, Patrick Minx, Philippe Latreille, Holland Cordum, Andrew Van Brunt, Kyung Kim, Robert S Fulton, Lucinda A Fulton, Sandra W Clifton, Richard K Wilson, Robin D Knight, Jeffrey I Gordon

(A) Genes involved in core metabolic processes are enriched among non-laterally transferred genes identified by a phylogenetic approach (see Materials and Methods). The proportion of genes identified as not laterally transferred in each genome (light blue), as well as assigned to the GO terms “Primary metabolism” (yellow) and “Protein biosynthesis” (red), are shown. Significant increases (enrichment) relative to each whole genome are shown by an upward-pointing arrowhead, and decreases (depletion) by a downward-pointing arrowhead, whereas the corresponding probability, determined by a binomial test, is denoted by asterisks: a single asterisk (*) indicates p < 0.05; double asterisks (**) indicate p < 0.01; and triple asterisks (***) indicate p < 0.001.

(B) Laterally transferred genes are enriched among genes assigned to the GO term “DNA methylation” (e.g., restriction-modification systems) (red), relative to each complete genome (light blue). Glycosyltransferases (yellow) and genes located within CPS loci (green) are also enriched within the set of transferred genes. Significance was determined and denoted as in (A).

(C) B. distasonis (light blue) possesses a significantly larger proportion of laterally transferred genes than the other Bacteroidetes, as shown by significant increases in the proportion of genes in each category of our analysis (“LGT in,” laterally transferred into the genome; “Novel,” no homologs identified from other species; “LGT direction unresolved,” laterally transferred but direction unknown; “LGT out,” laterally transferred out of the genome; and “Unresolved,” lateral transfer uncertain; see Materials and Methods for detailed explanations of categories and for a complete list of genes in each category). Significant changes, denoted as in (A), were determined by a binomial test, using the average proportion within all other genomes used in the analysis as the reference. Other strains are B. vulgatus (red), B. thetaiotaomicron (yellow), B. fragilis NCTC 9343 (green), B. fragilis YCH 46 (purple), and P. gingivalis (orange).

(D) A prominent laterally transferred locus within B. distasonis contains a ten-gene hydrogenase complex, likely allowing B. distasonis to use hydrogen as a terminal electron acceptor in anaerobic respiration. Genes transferred into B. distasonis are colored red, whereas genes whose phylogeny could not be resolved are shown in yellow. Letters indicate functional components of the hydrogenase complex: L, large subunit; M, maturation or accessory factor; and S, small subunit.