NIME Array Percentage G + C Content Profile for an Array Located at 1283600–1284640 bp in the FAM18 Genome

<p>The % G + C window size is 24 bases. Maximum, minimum, and median are also shown. Red blocks represent dRS3 with inverted repeats indicated by grey triangles. Blue blocks represent RS elements.</p

Rearrangements between the Meningococcal Genomes

<p>The dotplots were generated using MUMmer version 3.15 (<a href="http://mummer.sourceforge.net" target="_blank">http://mummer.sourceforge.net</a>) and indicate matching sequences with codirectional and reversed regions of synteny shown in red and green, respectively. Genome sequences are aligned to start/finish at the origin of replication with the approximate position of the terminus of replication indicated (Ter) (note this required rotation of the publicly available sequences for Z2491 and MC58, see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030023#s3" target="_blank">Materials and Methods</a>). Also shown are the positions of the foci of the three major inversion events (IE1, IE2, and IE3, see text for detail).</p

Sequence Divergence in Orthologues Flanking Repeat Arrays<b> </b>

<div><p>(A) Plot of repeat array length against flanking orthologue sequence identity for FAM18 versus Z2491 (blue diamond), Z2491 versus MC58 (red square), and FAM18 versus MC58 (green triangle).</p><p>(B) Plot of distance from array versus orthologue identity for FAM18 versus Z2491, Z2491 versus MC58, and FAM18 versus MC58.</p><p>(C) The same as (B), ignoring the first CDS.</p></div

Pie Charts Showing Association between Repeat Arrays and Surface Proteins in FAM18

<p>Chart sectors are coloured according to gene function (see colour key).</p

Distribution of Orthologous CDSs in Y. enterocolitica 8081, Y. pestis CO92, and Y. pseudotuberculosis IP32953

<div><p>The Venn diagram shows the number of genes unique or shared between two other <i>Yersinia</i> species (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020206#s4" target="_blank">Materials and Methods</a>). The associated pie charts show the breakdown of the functional groups assigned for CDSs in relevant sections of the Venn diagram. Colour code for the pie charts is as follows: hypothetical proteins (1); conserved hypothetical proteins (2); chemotaxis and motility (3); chromosomal replication (4); chaperones (5); protective responses (6); transport and binding proteins (7); adaptations to atypical conditions (8); cell division (9); macromolecule degradation (10); synthesis and modification of macromolecules (11); amino acid biosynthesis (12); biosynthesis of cofactors, prosthetic groups, and carriers (13); central intermediary metabolism (14); small-molecule degradation (15); energy metabolism (16); fatty acid biosynthesis (17); nucleosides and nucleotide biosynthesis and metabolism (18); periplasmic/exported/lipoproteins (19); ribosomal proteins (20); laterally acquired (including prophage CDSs) (21); pathogenicity and virulence (22); general regulation (23); and miscellaneous function (24).</p><p><i>Y. en, Y. enterocolitica</i> strain 8081; <i>Y. pstb, Y. pseudotuberculosis</i> strain IP32953; <i>Y. pestis, Y. pestis</i> strain CO92<i>.</i></p></div

Microarray Analysis of the Plasticity Zone of 34 Isolates of Y. enterocolitica Biotypes 1A, 1B, 2, 3, and 4

<p>Microarray analysis of the genomic DNA from 34 Y. enterocolitica isolates, representing five biotypes, constructed using GeneSpring version 6.1 software. Data is presented for the CDS in the range of YE3439–YE3658 including the PZ and YGI-1, as marked (left side). Each numbered column represents the results from a different Y. enterocolitica strain: 1, 09/03; 2, 12/02; 3, 208/02; 4, 35/03; 5, 77/03; 6, 30/02; 7, 81/02; 8, 14/02; 9, 119/02; 10, 212/02; 11, 218/02; 12, 231/02; 13, 56/03; 14, 16/03; 15, 209/02; 16, 149/02; 17, 177/02; 18, 153/02; 19, 202/02; 20, 7/03; 21, 135/02; 22, 8/03; 23, 190/02; 24, 220/02; 25, 227/02; 26, 201/02; 27, Y30; 28, Y73; 29, Y89; 30, Y71; 31, Y68; 32, Y70; 33, Y69; and 34, 8081 (control). See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020206#pgen-0020206-st002" target="_blank">Table S2</a> for details. The colour-coded biotype key for each isolate is shown at the bottom. Each row represents an individual gene within this region. Coloured blocks (right side) have been used to highlight groups of CDSs showing differing distributions between isolates. The range of CDSs encoded within these blocks is shown (in brackets). Also marked are the relative positions of interesting CDSs or loci that have been mentioned within the body of this article. Blue CDSs correspond to those genes that are considered absent/divergent, and yellow CDSs correspond to genes that are assigned present/conserved. Grey indicates data not obtained.</p