Additional file 2: Figure S2. of Complete genome anatomy of the emerging potato pathogen Dickeya solani type strain IPO 2222T

Symptoms of D. solani IPO 2222T on potato plants (a) and tubers (b). (TIFF 8904 kb

A new oxolane from <i>Enterobacter cloacae</i>

<p><i>Enterobacter cloacae</i> is a highly pathogenic Gram-negative proteobacterium which is responsible for a wide array of infections. In the present study, the fermentation culture of <i>E. cloacae</i> has yielded one new oxolane compound, Rimboxo (<b>1</b>) in addition to three known compounds, i.e. Maculosine (<b>2</b>), phenylacetic acid (<b>3</b>) and methyl myristate (<b>4</b>). These compounds were isolated and characterised using extensive chromatographic and spectroscopic methods, and were subjected to cytotoxicity evaluations.</p

Protein sequence comparison of prophage large terminase and phage tail-measure protein.

<p>A: <i>Bacillus cereus</i> VD154 (gi|446509997). B: <i>Bacillus cereus</i> AH1272 (gi|488006653). C: <i>Bacillus thuringiensis</i> (gi|384182753). D: <i>Bacillus virus</i> 1 (gi|155042934). E: <i>Geobacillus</i> phage GBSV1 (gi|115334627). F: <i>Geobacillus thermoglucosidasius</i> C56-YS93 (gi|336234248). G: <i>Geobacillus</i> sp. Y412MC52 (gi|261418101). H: <i>Geobacillus</i> sp. Y4.1MC1 (gi|312109743). I: <i>Paenibacillus mucilaginosus</i> K02 (gi|511629193). J: <i>Bacillus cereus</i> AH1271 (gi|488002245). K: <i>Bacillus cereus</i> VD156 (gi|446819371). L: <i>Bacillus sonorensis</i> L12 (gi|493686871). M: <i>Bacillus methanolicus</i> PB1 (gi|490573477). N: <i>Geobacillus kaustophilus</i> HTA426 (gi|56419074). O: <i>Geobacillus virus</i> E2 (gi|148747742). P: <i>Clostridium ljungdahlii</i> DSM 13528 (gi|300853566).</p

The gene cluster of various GHs, transporters, transcriptional regulators, and transcriptional repressors in <i>Anoxybacillus</i> sp. SK3-4.

<p>Identical clusters of genes are present in other <i>Anoxybacillus</i> species.</p

Presence of gene clusters of NarGHJI and NasBC in <i>Anoxybacillus</i>, <i>Geobacillus</i>, and <i>Bacillus</i>.

<p>+ present;</p><p>− absent.</p

Subsystem feature counts according to the SEED classification.

<p>A: Cofactors, vitamins, prosthetic groups, pigments. B: Cell wall and capsule. C: Virulence, disease, and defense. D: Potassium metabolism. E: Photosynthesis. F: Miscellaneous. G: Phages, prophages, transposable elements, plasmids. H: Membrane transport. I: Iron acquisition and metabolism. J: RNA metabolism. K: Nucleosides and nucleotides. L: Protein metabolism. M: Cell division and cell cycle. N: Motility and chemotaxis. O: Regulation and cell signaling. P: Secondary metabolism. Q: DNA metabolism. R: Regulons. S: Fatty acids, lipids, and isoprenoids. T: Nitrogen metabolism. U: Dormancy and sporulation. V: Respiration. W: Stress response. X: Metabolism of aromatic compounds. Y: Amino acids and derivatives. Z: Sulfur metabolism. ZA: Phosphorus metabolism. ZB: Carbohydrates. Black: <i>Anoxybacillus</i> sp. SK3-4; red: <i>Anoxybacillus</i> sp. DT3-1; blue: <i>Anoxybacillus flavithermus</i> WK1; green: <i>Anoxybacillus flavithermus</i> TNO-09.006; orange: <i>Anoxybacillus kamchatkensis</i> G10.</p

Sequence arrangements of prophages in <i>Anoxybacillus</i> genome as identified by PHAST.

<p>(<b>A</b>) ProphageWK of <i>Anoxybacillus flavithermus</i> WK1. (<b>B</b>) ProphageG10 of <i>Anoxybacillus kamchatkensis</i> G10. (<b>C</b>) ProphageSK of <i>Anoxybacillus</i> sp. SK3-4. (<b>D</b>) ProphageDT of <i>Anoxybacillus</i> sp. DT3-1. ProphageWK and prophageG10 may not be intact prophages, due to the lack of putative genes encoding morphological proteins. This is in contrast to intact prophageSK and prophageDT, which have more and ordered morphological genes. These morphological genes are arranged in clusters or modules, which is a hallmark of prophage sequences, and in an order typical of temperate tailed-phage genomes. Note that prophageDT is located on the complementary strand of <i>Anoxybacillus</i> sp. DT3-1. The prophage map was reversed for ease of reference. Both prophageSK and prophageDT also share six genes (shown in figure) that appear to be conserved in location and order. The details of ORFs information for prophageSK and prophageDT are provided in <b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090549#pone.0090549.s001" target="_blank">Table S1</a></b> and <b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090549#pone.0090549.s002" target="_blank">Table S2</a></b>.</p

Genome features of the <i>Anoxybacillus</i> species used in this study.

<p>Genome features of the <i>Anoxybacillus</i> species used in this study.</p

Phylogenetic tree of selected <i>Bacillaceae</i> based on concatenated sequences of 361 orthologs.

<p>Phylogenetic tree of selected <i>Bacillaceae</i> based on concatenated sequences of 361 orthologs.</p

Genomes comparison of <i>Anoxybacillus</i> species.

<p>(<b>A</b>) Five-way Venn-diagram showing the number of shared and specific CDS among the <i>Anoxybacillus</i> spp. Orthologous groupings were based on 50% identify cutoff and overlap of at least 70% protein sequence length. (<b>B</b>) BRIG image with <i>Anoxybacillus</i> sp. SK3-4 genome sequence set as the central reference. (<b>C</b>) BRIG image with <i>Anoxybacillus</i> sp. DT3-1 genome sequence set as the central reference.</p