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Fig. 5 | Journal of Genetic Engineering and Biotechnology

Fig. 5

From: De novo assembly and comparative genome analysis for polyhydroxyalkanoates-producing Bacillus sp. BNPI-92 strain

Fig. 5

a Phylogenetic tree and evolutionary relationships of taxa for Bacillus sp. BNPI-92 and the other closely related strains. The evolutionary history was inferred using the neighbor-joining method [45]. The optimal tree with the sum of branch length = 0.18016536 is shown. Evolutionary distances were calculated by neighbor-joining and based on 1000 bootstrap replication of confidence values (percentage of 1000 replication). Bar, 0.05 substitutions per nucleotide position [46]. The evolutionary distances were computed by using p-distance method [47]. The analysis involved six nucleotide sequences. All positions containing gaps and missing data were eliminated. Finally, evolutionary analyses were performed with MEGA7.0.9 software [48]. Micrococcus luteus DSM 20030 T (AJ536198.1) was designated and used as outgroup in the analyses; other related sequences were obtained from EzTaxon-e server and annotated using RAST server before tree construction b UPGMA dendrograms heatmap for OrthoANI [17], c UPGMA dendrograms heatmap for OriginalANI [17] and d UPGMA dendrograms heatmap for genome to genome distance calculator (GGDC) [17]. e In silicon DDH ( is DDH) for Bacillus sp. BNPI-92 and closely related strains. In silicon DDH analysis was performed using online tool that is available at https://tygs.dsmz.de/and Fig. 8e constructed using GraphPad Software. f Average nucleotide identity (ANI) (%) between pairs of Bacillus sp. BNPI and other five strains. ANI values of ≥ 96% and is DDH values of ≥ 70% consistently grouped genomes originating from strains of the same species together. It was performed according to Goris et al . [31] and using online tools that are available at http://enve-omics.ce.gatech.edu/ani/

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