33%). These other duplications were found primarily in β-Proteobacteria (3.33%) and γ-Proteobacteria (7.22%); as shown in Figure 7. Table 1 Distribution of Tree Types and Bootstrap Values in R. C188-9 mouse sphaeroides CI-CI CI-CII CII-CII Duplicated Genes 116 62 11 A-Type B-Type A-Type B-Type A-Type B-Type v ≥ 90 101 9 47 11 8 3 70 ≤ v < 90 3 0 0 1 0 0 v < 70 1 2 1 2 0 0 Total 105 (91.5%) 11 (9.5%) 48 (77.4%) 14 (22.6%) 8 (72.7%) 3 (27.3%) Note: Bootstrap Value = v Figure 7 Distribution of the highest ortholog matches for Type-A gene duplication PARP inhibitor matches. The Proteobacteria groups are abbreviated to their subdivision. The amount of proteins in each group is shown on top of the columns
while the y-axis depicts the percentage selleck screening library of the total amount that each column constitutes. The number of significant matches (meeting the designated criteria mentioned in the Materials and Method section) of R. sphaeroides
2.4.1 query protein sequences to three other R. sphaeroides strains (ATCC 17025, ATCC 17029, and KD131) was also determined (Additional file 3). The results show that there is significant variability with levels of gene loss and gene retention. Merely 28 (11.97%) of the 234 queries had only two gene matches, representing a duplication pair, in all three strains. 26 (92.86%) of these 28 possessed Type-A gene topology while only 2 (7.14%) possessed Type-B topology. In 144 (61.54%) of the 234 queries, at least one strain had two matches; 122 (84.72%) of the 144 displayed Type-A topology while 22 (15.28%) represented Type-B trees. Figure 8 details the distribution of the matches for the three strains. The match
distribution reveals varying levels of gene retention among the organisms. A good deal of genes in the three strains (40 – 50 genes) Dehydratase presented zero matches suggesting that either these genes have been lost from the organisms or they have sufficiently diverged as to not present significant homology to their strain counterparts. In addition, R. sphaeroides ATCC 17029 has a much lower number of 2 matches (67) and higher numbers of 0 matches (50) and 1 match (100) in relation to those of the other strains. Figure 8 The distribution of matches to the R. sphaeroides 2.4.1 query sequences. BLASTP analysis with each single gene in each of the 234 duplicate gene pairs was performed against three other R. sphaeroides strains (ATCC 17025, ATCC 17029, KD131). The matches that met the specified criteria were kept and examined accordingly. The picture depicts varying levels of gene loss and retention among each of the strains. Figure 9 provides four expanded phylogenetic trees with genes from all four R. sphaeroides species (2.4.1, ATCC 17025, ATCC 17029, and KD131) along with two related genes from species outside of R. sphaeroides (orthologs). These genes in the other R. sphaeroides strains were also only present in only two copies.