12 research outputs found
Gene cluster containing TerY-P triad conserved among three <i>H</i>. <i>pylori</i> strains and two other bacteria.
No full textOrthologous genes are drawn with the same colors. Gene numbers or names are presented in or near the arrows. Regions of sequence similarity between loci are indicated by red bands. The diagram was drawn using GenomeMatcher [47].</p
The number of OGs classified in each mobility class.
No full text(A) Histogram showing the strain number distribution of each mobility class among non-unique accessory OGs. The histogram is equivalent to Fig 1(A) except the rightmost bar representing the universal core OGs (num_strain = 30) and the leftmost bar representing the unique OGs (num_strain = 1) are eliminated. (B) Frequencies of the mobility classes among the accessory OGs in each strain. The order of strains is same as in S1 Table. Note that each strain also has the same number (1248) of universal core OGs that are not shown in this graph.</p
Chromosomal context of CGCs.
No full text(A) CGC-2 and CGC-5 (bacteriophage 1961P). (B) CGC-3 (the cluster containing TerY-P triad). Genes in the target CGCs are centered and colored cyan. In the flanking regions, genes in the syntenic core are colored according to the location in the reference genome (whose strain name shown in the left side is colored red). Thus, for a Mobile class CGC (such as CGC-5), the flanking core genes are assigned different colors in different strains.</p
Pan-genome and core genome among <i>Helicobacter pylori</i>.
No full text(A) Histogram showing the distribution of the number of strains in each OG among the 30 strains. Sets of OGs corresponding to pan-genome, universal core, accessory, and unique OGs are indicated. (B) Sizes of the syntenic core, universal core, and pan-genome as functions of the number of strains. An ordered lists of the 30 strains was randomly generated and the sets of n strains (n = 2,4,…,30) generated from this list was subject to core- and pan-genome analysis. The test was repeated 20 times and the average numbers of core- and pan-genome sizes were plotted with error bars that represent standard deviations. Syntenic core between two genomes is not well defined and thus is not plotted. (C) The number of new OGs added to the pan-genome as a function of the number of strains. The number of new OG in n strains (n = 4,6,…,30) was calculated as the difference between the pan-genome size in n strains and that in n– 2 strains.</p
Integrating conjugative elements (ICEs).
No full text(A) Locations of ICE genes displayed on the RECOG system. Colors are assigned by CGC groups (CGC-4, red; 6, light green; 7, yellow; 8, magenta; 12, cyan; 15, purple; 19, brown; 23, blue; 26, dark green; other mobile OGs, dark gray). The strains are ordered such that the first 10 strains correspond to type ICEHptfs3 and the rest correspond to ICEHptfs4.(B) A phylogenetic network created from the concatenated sequence of three OGs, virB9, virB11 and virD4. (C) A phylogenetic network created from the putative DNA methyltransferase (DNMT) conserved in all ICE subtypes. Strain names are assigned colors according to the phylogeographical groups as in Fig 4.</p
Example of different RM systems occupying the same orthologous position.
No full text(A) Location of three RM systems designated A (blue; OG-81, 1424, 1544 and 1524 containing HP0050, HP0051, and HP0052 in strain 26695), B (green; OG-1668, 1667 and 1691 containing jhp0045 and jhp0046 in strain J99), and C (red; OG-1782, 1615, 1727 and 1785 containing HP0053 and HP0054 in strain 26695). See S2 Table for details of each OG. (B) A phylogenetic network created from the concatenated sequence of the RM-A. (C) A phylogenetic network created from the concatenated sequence of the RM-B. Strain names are assigned colors according to the phylogeographical groups as in Fig 4.</p
Definition of the mobility classes.
No full textGenes in the (syntenic) core OGs include the universal core genes (boxes in dark blue) and the remaining syntenic core genes (boxes in pale blue). Each core OG is assigned a core index (the above number) representing its order in the core alignment. Each of the non-core OGs (A, B, C, and D boxes) is assigned a pair of core indices representing the left- and right-neighboring core OGs. A set of genes that are located in the equivalent locus is enclosed in a box of a dashed line. The mobility_extent of each OG is defined as the number of distinct loci where the OG can be located, which is one for OG-A, three for OG-B, and one for OG-C. Note that we ignored the genes in OG-C in genomes 4 and 5 in which the difference between the left- and right-neighboring core indices is too large (non-consecutive), which indicates that the gene is located around a break point of a large rearrangement (in these cases, inversion and transposition). OG-D appears in only one genome and thus is classified as Unique. Mobility class is defined on the basis of mobility_extent and Ng (see text), where Ng is the effective number of genes obtained by the following calculation: (number of genes in OG)–non-consecutive.</p
Neighboring co-occurring gene clusters (NCGCs).
No full textNeighboring co-occurring gene clusters (NCGCs).</p
Co-occurring gene clusters (CGCs).
No full text(A) The 60 CGCs ordered according to the cluster size (the number of OGs included). An occurrence pattern represents presence/absence of CGC in each strain where a large box indicates that the strain contains all OGs in the CGC and a small box indicates that the strain contains only part of the OGs. In the occurrence pattern, strains are ordered in the same way as in S1 Table and colors are assigned according to the phylogeographical groups in the same way as in Fig 4. (B-F) The five largest CGCs displayed on the RECOG system. (B) CGC-1 corresponding to cag pathogenicity island; (C) CGC-2 corresponding to a part of bacteriophage 1961P; (D) CGC-3 containing protein kinase C and protein phosphatase C2 homologs; (E) CGC-4 corresponding to a part of ICE containing type IV secretion system; (F) CGC-5 corresponding to a part of bacteriophage 1961P. The left part shows a hierarchical clustering tree based on the occurrence pattern similarity. The central part shows occurrence patterns, where the order of strains is same as in (A), and the colors are assigned according to the neighboring clustering, i.e., the cells filled in the same color in each column contain genes that are closely located on the chromosome (here, we used 8000 bp window for the neighborhood criterion). Enlarged figures B-F are shown in S1 Fig.</p
