Neighbor-Joining Tree Based on the GTR+G+I Evolutionary Model for 3,406 bp Sequences from 58 Strains of H. pylori and Four Strains of H. acinonychis

<p>The tree shows the phylogenetic relationships between H. acinonychis and populations within <i>H. pylori,</i> and arrows indicate the three strains, J99, 26695, and Sheeba, from which genome sequences are currently available. This phylogenetic tree indicates that H. pylori (lines) and H. acinonychis (lines plus red dots) are closely related but cannot resolve the direction of ancestor-descendent relationships. Genetic distance scale bar at bottom.</p

Fragmentation Patterns in Ten Genes among Three H. acinonychis Strains

<p>Ten genes that are intact in 26695 but are fragmented in the Sheeba genome (subgroup B) were re-sequenced from strains t1 and HA5141 of subgroup B and BombayA of subgroup A. Black lines indicate sequenced fragments and thick blue arrows indicate CDSs of ≥140 bp. Designations at the top indicate CDS designations in 26695 whereas designations above the Sheeba sequences indicate both the protein name and the CDS designations in Sheeba (Hac0035, Hac0036, etc.).</p

Hybridization of a DNA Microarray Chip Containing 99 PCR Products against Representative Strains of H. acinonychis and H. pylori

<p>Six strains of H. acinonychis from subgroups A and B and 21 strains that represent the genetic diversity of H. pylori (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020120#pgen-0020120-st005" target="_blank">Table S5</a>) were tested for hybridization (yellow) or lack of hybridization (red) with 99 PCR products (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020120#pgen-0020120-st006" target="_blank">Table S6</a>) from genes that are present in Sheeba and lacking in 26695 and J99. The results were clustered according to genes (left) and strains (top). Genes that hybridize exclusively with all H. acinonychis strains are summarized as group I (right), genes hybridizing only with some H. acinonychis are in group II and genes hybridizing with some H. pylori are in group III. Where gene functions were attributed, they are indicated at the right and other genes encode hypothetical proteins. black, missing data.</p

Gene Fragmentation, Duplication, and Import

<div><p>(A) Fragmentation of the <i>vacA</i> (vacuolating cytotoxin) gene (red) into 13 fragments and import of <i>neuACB, cst, cst</i> (blue-green) within Sheeba. <i>neuACB</i> encode acylneuraminate cytidyltransferases and <i>cst</i> encodes a sialyltransferase.</p><p>(B) Translocation of a duplicate of the fragmented <i>vacA</i> gene to a different genomic location. The duplicated <i>vacA</i> gene (red) contains the same fragmentation pattern and differs by only one sequence polymorphism in 3,815 bp from that in part A, indicating that the duplication is recent and occurred after the fragmentation event. Next to the duplicated <i>vacA</i> gene are located three genes (light blue) that are unique to H. acinonychis.</p><p>(C) Homologies of the <i>neuACB, cst, cst</i> gene cluster from part A with syntenic clusters in C. jejuni NCTC11168 and the B. cereus virulence plasmid pBC218.</p></div

Similarities between the Genomes of H. acinonychis Sheeba and H. pylori 26695 and J99

<div><p>(A) Venn diagram of genomic properties. Numbers in red within each arc represent numbers of genes, each of which may contain multiple CDSs if the corresponding gene is fragmented.</p><p>(B) Age calculations since a common ancestor (LCA) based on synonymous pair-wise distances for 612 conserved genes according to the methods of Li et al., 1985 and the modified Nei-Gojobori method.</p><p>(C) Frequencies of normalized blast scores in pair-wise comparisons between Sheeba and three other genomes.</p></div