Edited by Jeffrey I. Gordon, Washington University School of Medicine, St. Louis, MO, and approved July 29, 2009
↵1K.T.K, M.H.S., M.F.R., and J.L.M.R contributed equally to this work. (received for review February 25, 2009)
The 10 Shewanella genomes used in this study and their evolutionary gradient. The geographic origin (A) and the 16S rRNA-based phylogenetic tree (B) of the 10 genomes (in boldface type) are shown. The scale represents the number of substitutions per position, and the numbers above and below the nodes represent the bootstrap support from 1000 resamplings using parsimony and maximum likelihood methods, respectively. Bootstrap values <50 were omitted. A continuous genetic gradient was formed (C) when the fraction of the total genes in the genome shared between two genomes (y axis) was plotted against the ANI of the shared genes between the two genomes (45 comparisons in total are shown). Dashed blue lines represent the 90% prediction intervals of the regression line; open squares identify the outlier pairs of genomes observed (discussed in the text).
The Shewanella pangenome. (A) Contribution of different categories of genes to the pangenome as a function of ANI. The genes that differed in all pairwise whole-genome comparisons among the 10 Shewanella genomes (45 comparisons in total) were assigned to five major functional categories (graph legend). The number of genes in each category, expressed as a fraction of the total genes that differed between the two genomes (y axis), is plotted against the genomic ANI value of the two genomes compared. Individual data points representing each comparison have been removed for clarity; trendlines representing the mean, and bars representing one standard deviation from the mean, are shown instead. (B) Comparisons with the enterics pangenome. The number of genes that remained conserved (y axis) with the inclusion of more genomes in the analysis is plotted against the number of genomes (x axis) used (light colors). The total number of nonredundant unique genes in all genomes used is also shown (dark colors). Bars represent one standard deviation based on 10 random combinations in adding the genomes to the analysis.
Genome vs. proteome comparisons among nine Shewanella strains. The protein profiles of nine Shewanella strains were compared based on the 2128 core genes (A) and the 4300 genes found in the genome of strain MR-1 (B) for gene expression, and the nine strains were subsequently clustered based on their overall similarity in the expression patterns of these two gene sets as follows. For each gene set, a full (all genes by all genomes) 0/1 matrix was built, with “1” denoting expression (defined as the detection of at least two unique peptides per protein) and “0” denoting no expression of the corresponding protein; the derived matrices were clustered as described in the SI Materials and Methods and the resulting cladograms are shown. Similarly, the nine strains were also clustered based on the presence/absence of the 4300 MR-1 gene orthologs in their genome (sequence comparisons, C). A maximum-likelihood phylogenetic tree of the concatenated alignment of 1507 single-copy core genes that had no detectable signal for recombination by Phi test analysis (22) is also shown (D). Scale bars represent percent similarity in the derived matrices for (A), (B), and (C); and number of substitution per site for (D).
Modeling bacterial genotypic and phenotypic conservation across an evolutionary gradient. The presence of orthologous proteins, TonB outer membrane receptors, cytochromes, methyl-accepting chemotaxis proteins (MCPs), transcriptional regulators, metabolic pathways, protein expression patterns, and reduction of metal or metalloids (anaerobic growth) was determined for the 10 Shewanella strains (see Materials and Methods). Each of the traits was compared among the Shewanella strains in a pairwise manner (45 comparisons in total). The fraction of shared traits was determined for each pair of strains and plotted against the average nucleotide identity (ANI) of the respective strain pair. Inset graph depicts the relationships between conservation of the traits and evolutionary distance using linear regression trendlines adjusted to intersect with the x and y axis at 100%. The r2 values of the regressions are also shown.
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