arsenaticum. Table 6 Summary of genome: one chromosome and one extra-chromosomal element Table 7 Genomic inversions present within the sampled population The majority of the P. oguniense genome is structurally syntenic to the genome of P. arsenaticum, and genes found in both species show an average of approximately selleck products 96% nucleotide identity. The P. oguniense genome is approximately 15% larger than P. arsenaticum, with the former encoding 536 more (2835 – 2299) open reading frames (ORFs) predicted to be genes. Vast stretches of sequence space are syntenic between the two species (Figure 2, regions in blue), broken by relatively few regions that appear to arise from either gene loss in P. arsenaticum or genomic expansion in P. oguniense, possibly a result of the numerous paREP elements present in these genomes (Figure 2).

These repetitive regions are difficult to assemble, and some are putative transposons (PaREP2b, for example). Figure 2 Genomic alignment of P. oguniense with P. arsenaticum. Outer ring: P. oguniense (+ strand); Inner ring: P. arsenaticum (- strand). Inter-species alignment blocks shown in light blue and gold (inverted orientation). Intra-species P. oguniense genomic inversions … We can identify specific genes and gene clusters that are present in P. oguniense but are missing in P. arsenaticum. Notably, the cobalamin synthetic cluster and two thiamine synthetic genes (ThiW and ThiC) are absent in P. arsenaticum. The terminal cytochrome cluster associated with aerobic respiration [35] is also absent in P. arsenaticum as expected from an obligate anaerobe.

Among the 16 largest deletions in P. arsenaticum (relative to P. oguniense), four are associated with paREP2 genes, six with paREP1/8, and one with paREP6 (Table 5). Conclusion Genomic sequencing and assembly of Pyrobaculum oguniense has yielded a complete genome and an extra-chromosomal element. The main chromosome is largely syntenic to Pyrobaculum arsenaticum and contains a number of gene clusters that are absent in that species. This is of particular interest considering that these species were isolated on opposite sides of the Eurasian continent; P. oguniense was isolated in Japan, while P. arsenaticum was isolated in an arsenic-rich anaerobic pool in Italy. The synteny that has been retained between the genomes of P. oguniense and P.

arsenaticum allows a close examination of gene gain or loss events in the genetic history of these two species. P. arsenaticum is missing the gene clusters that support cobalamin and thiamine synthesis, and it is missing the aerobic cytochrome cluster. Given that P. oguniense and the next closest member in the clade, P. aerophilum, have both retained these capabilities; Drug_discovery the most parsimonious explanation is gene loss in P. arsenaticum. Because these genes are located at disparate positions in the P.