Pping to 55 before entering Wairakei Stream. As the water cools down, silica sinter deposits subaqueously in the channels, forming precipitates composed of amorphous silica (opal-A) [9]. The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life [13]. Although bacteria are believed to play only a passive role in silicification, they definitely affect the absolute rate of silica precipitation by providing increased surface area. In addition, bacteria largely control the textural features of the resulting siliceous sinters [14]. We have obtained the complete genome sequence of A. flavithermus WK1 and employed it to analyze bacterial physiology and its changes in response to silica-rich conditions. This study sheds light on the biogeochemical processes that occur during the interaction between microbial cells and dissolved silica and result in sinter deposition.ResultsGenome organizationThe genome of A. flavithermus strain WK1 consists of a single, circular chromosome of 2,846,746 bp (Figure 1) with an average G+C content of 41.78 (Table 1). The genome encompasses 2,863 predicted protein-coding genes, 8 rRNA (16S-23S-5S) operons, 77 tRNA genes, and 19 predicted riboswitches. Of the 2,863 predicted proteins, 1,929 have been assigned probable biological functions, 418 were conserved proteins with only general function predicted, and for 516 putative proteins no function was predicted (of these, 110 proteins had no detectable homologs in the NCBI protein database). The genome contains one prophage region withGenome size G+C content SCH 530348 site Number of predicted coding sequences Average size of coding sequences Percentage coding Number of protein coding genes Number of proteins with assigned biological function Number of proteins with predicted general function Number of proteins of unknown function Number of proteins assigned to COGs Number of tRNA genes Number of PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/28859980 rRNA operons Number of small RNA genes Number of riboswitches2,846,746 bp 41.78 2,863, 104 RNA, 112 pseudogenes 860 bp 90.2 2,863 (22 with frame shifts) 1,929 (67 ) 418 (15 ) 516 (18 ) 2,526 (88 ) 77 24 3Genome Biology 2008, 9:Rhttp://genomebiology.com/2008/9/11/RGenome Biology 2008,Volume 9, Issue 11, Article RSaw et al. R161.C COG D COG E COG F COG G COG H COG I COG J COG K COG L COG M COG N COG O COG P COG Q COG R COG S COG T COG Unknown COG CDS tRNA rRNA GC content GC skew+ GC skew-2,500 kbp 500 kbpAnoxybacillus flavithermus2,000 kbp2,846,746 bp1,000 kbp1,500 kbpFigure representation of the A. flavithermus genome Circular1 Circular representation of the A. flavithermus genome. The first and second circles show open reading frames (ORFs) in the positive strand: the first circle shows ORFs categorized by COG functional categories and the second circle shows coding sequences in blue and tRNA/rRNA genes in dark red. The third and fourth circles show ORFs in a similar fashion to the first and second circles but in the negative strand. The fifth circle shows variations in G+C content of the genome from the mean. The sixth circle shows a GC-skew plot of the genome showing approximate origin of replication and termination sites.Genome Biology 2008, 9:Rhttp://genomebiology.com/2008/9/11/RGenome Biology 2008,Volume 9, Issue 11, Article RSaw et al. R161.genes (Aflv_0639-0682) and encodes 105 transposases. In its gene ord.
