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1.
Figure 6

Figure 6. From: The Salmonella enterica Pan-genome.

Heatmap of SPI conservation. SPIs from the Pathogenicity Island Database were aligned against genomes, and the average identity of all proteins in each SPI was hierarchically clustered in two dimensions. The vertical axis lists the SPIs while the genomes are located horizontally

Annika Jacobsen, et al. Microb Ecol. 2011 October;62(3):487-504.
2.
Figure 4

Figure 4. From: The Salmonella enterica Pan-genome.

Flowerplot of unique gene families in each Salmonella serovar. The figure presents the average number of gene families found in each genome as being unique to the serovar. Also given is the size of the core genome. The color of the petals represents the S. enterica serogroups (see Table 1 for key)

Annika Jacobsen, et al. Microb Ecol. 2011 October;62(3):487-504.
3.
Figure 3

Figure 3. From: The Salmonella enterica Pan-genome.

Pan- and core genome plot of 35 Salmonella strains. The red and blue lines show the progression in the core and pan genomes as more and more genomes are considered, while the columns indicate the amount of novel gene families encountered. The color of the columns represents the serogroup as defined in Table 1 (see Table 1 for key)

Annika Jacobsen, et al. Microb Ecol. 2011 October;62(3):487-504.
4.
Figure 7

Figure 7. From: The Salmonella enterica Pan-genome.

Pan genome family trees based on the absence and presence of gene families. In the upper panel, the tree is constructed by weighting gene families higher the more genomes they are present in. The lower panel shows the opposite scheme where genes present in smaller numbers are weighted higher. The serogroup colors are defined in Table 1

Annika Jacobsen, et al. Microb Ecol. 2011 October;62(3):487-504.
5.
Figure 1

Figure 1. From: The Salmonella enterica Pan-genome.

BLAST Matrix of 35 S. enterica genomes. The figure shows the number of gene families found in common between the Salmonella strains and the degree of gene duplication within each by pairwise all-against-all BLAST comparisons at the amino acid level. A higher resolution version is available in the Supplemental Section with additional data viewable under zoom

Annika Jacobsen, et al. Microb Ecol. 2011 October;62(3):487-504.
6.
Figure 2

Figure 2. From: The Salmonella enterica Pan-genome.

Phylogenetic analysis of 16S rRNA. (Left) 16S rRNA tree of different genus in the enterobacteria family, Salmonella is marked with color. (Right) 16S rRNA tree of 27 Salmonella genomes, colors indicate serogroups (see Table 1 for key). The Salmonella genomes of Table 1 which are not presented here are absent because full length 16S rRNA could not be identified in most draft genomes (see “Materials and methods”). The bootstrap values, based on 1,000 iterations, are shown in red numbers, next to the branches

Annika Jacobsen, et al. Microb Ecol. 2011 October;62(3):487-504.
7.
Figure 5

Figure 5. From: The Salmonella enterica Pan-genome.

BLAST atlases of the 35 S. enterica and two E. coli. a BLAST atlas with S. Typhimurium str. D23580 as reference, representing the generalist strains. Six SPIs are marked on the atlas. b BLAST atlas with S. Typhi str. Ty2 as reference, representing a host-specific serovar. Four SPIs that were published along with the genome sequence are marked on the atlas. Generally, the Salmonellas show high homology with a few variable regions as SPIs. Also marked are several poorly characterized gene islands, I-a to VI-a and I-b to III-b (additional information in the Supplementary Section)

Annika Jacobsen, et al. Microb Ecol. 2011 October;62(3):487-504.

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