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Fig. 3 | BMC Genomics

Fig. 3

From: Whole genome de novo sequencing and comparative genomic analyses suggests that Chlamydia psittaci strain 84/2334 should be reclassified as Chlamydia abortus species

Fig. 3

Circular representation of the C. psittaci 84/2334 plasmid sequence and comparative phylogenetic analysis. a Circular representation of the plasmid sequence of strain 84/2334; Circles from the outside in show: the positions of the eight coding sequences on the forward (circle 1) and reverse (circle 2) strands of p84/2334. Circles 3–5 show positions of BLAST hits determined through blastn comparisons of C. psittaci 6BC (circle 3), VS225 (circle 4) and M56 (circle 5) with the following settings: query split size = 50,000 bp, query split overlap size = 0, expect value cut off = 0.0001. The height of the shading in the BLAST results rings is proportional to the percent identity of the hit. Overlapping hits appear as darker shading. Circles 6 and 7 show plots of the GC content and GC skew plotted as the deviation from the average for the entire sequence. The figure was generated using the program CGView. b Phylogenetic tree of an alignment of the plasmid sequences of C. psittaci (Cps), avian C. abortus (Cab), C. caviae (Cca), C. felis (Cfe) and C. pneumoniae (Cpn) strains. The consensus tree was estimated in TOPALi by Maximum Likelihood (PhyML) using a TIM + G substitution and rate heterogeneity model, according to BIC model selection, and 100 non-parametric bootstrap replicates. The tree is midpoint rooted and bootstrap support is indicated by the number at the node. The scale bar indicates the expected substitutions per site. Genotypes are given in square brackets. The tree was prepared in Dendroscope. Strain 84/2334 plasmid is in bold and red font. Avian C. abortus strain plasmids are in green font

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