Fig. 2
From: Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216T
Phylogenetic tree based on 16S rRNA gene sequences (left) and protein domains (right). A comparison is included (horizontal lines) between the two trees, showing the position of Bacillus smithii DSM 4216T relative to other Bacillus strains, as well as several industrially important Lactic Acid Bacterium strains. Only strains were used for which a complete genome sequence is available (as on 18 September 2014) in order to be able to perform the domain-based analysis. The 16S sequences were aligned using DECIPHER (R) [29] and the distance analysis was performed using a Jukes-Cantor correction. Phylogenetic analysis of all domains was performed by re-annotation of all proteins from selected genomes using InterProScan 5-RC7 and transformed into a absence-presence matrix. Distance was calculated using a standard Euclidean distance and clustering was performed by complete method using hclust. Tree comparison was performed by dendextend. Note that “unique” nodes between the 16S and domain-based tree are indicated with dashed lines (i.e. the order is the same but the subclustering is not). GenBank IDs of used whole genome sequences in order from top to bottom: AE016877.1, AL009126.3, CP000002.3, BA000004.3, CP012024.1, CP002472.1, CP002835.1, CP002293.1, CP001638.1, CP000557.1, CP006254.2, CP002442.1, CP002050.1, CP004008.1, CP003125.1, BA000043.1, CP000922.1, CP002222.1, CP001617.1