Journal: Standards in genomic sciences

Article Title: Complete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22(T).

doi: 10.1186/s40793-015-0099-5

Figure Lengend Snippet: Fig. 1 Phylogenetic tree based on 16S rRNA gene sequences of Pyrinomonas methylaliphatogenes K22T (highlighted) and other cultivated strains and clonal phylotypes within the phylum Acidobacteria. Four of the acidobacterial subdivisions are included. The tree was constructed via a Bayesian inference model (MrBayes), using Markov Chain Monte Carlo (MCMC - 2,000,000 resamples, four chains, temperature = 0.5) sampling methods to calculate posterior distributions of trees in the ARB software environment. Posterior probability values ≥90 % are indicated by open circles, ≥80 % by filled circles, and ≥70 % by open diamonds. The scale bar represents a 0.1 change per nucleotide position. Strains whose genomes have been sequenced, are marked with an asterisk; G. fermentans H5T (NZ_AUAU00000000), H. foetida TMBS4T (AGSB00000000), C. thermophilum BT (CP002414), P. methylaliphatogenes K22T (CBXV000000000), Candidatus ‘S. usitatus’ Ellin6076 (CP000473), Candidatus ‘K. versatilis’ Ellin345 (CP000360), Acidobacterium capsulatum ATCC 51196T (CP001472), Edaphobacter aggregans Wbg-1T (JQKI00000000), Granulicella mallensis MP5ACTX9T (CP003130), Granulicella tundricola MP5ACTX9T (CP002480), Terriglobus roseus KBS63T (CP003379), and Terriglobus saanensis SP1PR4T (CP002467). The phylotypes strains used as an outgroup included Thermoanaerobaculum aquaticum MP-01T (JX4200244), Dictyoglomus thermophilum H-6-12T (X69194), Caldisericum exile AZM16c01T (AB428365), Hydrogenobacter hydrogenophilus Z-829T (Z30424), Thermodesulfobacterium thermophilum DSM 1276T (AF334601), Deinococcus roseus TDMA-uv51 (AB264136), Truepera radiovicrix RQ-24T (DQ022076), Thermus aquaticus YT-1 (L09663), and Thermus scotoductus SE-1T (AF032127)

Article Snippet: Table 2 Project information MIGS ID Property Term MIGS-31 Finishing quality High quality draft MIGS-28 Libraries used Two libraries used: One 454 library, one Illumina PE library MIGS-29 Sequencing platforms 454 GS Junior Titanium, Illumina MiSeq MIGS-31.2 Fold coverage 75.0 × MIGS-30 Assemblers MIRA 4.0rc2 MIGS-32 Gene calling method Prodigal Locus tag PYK22 EMBL ID CBXV000000000 EMBL Date of Release 12 January 2015 GOLD ID Gp0050834 BIOPROJECT PRJEB4906 MIGS-13 Source Material Identifier DSMZ DSM 25857, ICMP ICMP 18710 Project relevance Microbial diversity of the Taupō Volcanic Zone, Tree of Life Insights from the genome sequence The P. methylaliphatogenes K22T genome assembly has a size of 3.79 Mb with a %G +C content of 59.3, both of which are comparable with the genomes of other sequenced Acidobacteria [24].

Techniques: Construct, Sampling, Software