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. 2025 Apr 9;10(5):e01496-24. doi: 10.1128/msystems.01496-24

Fig 2.

Circular genome maps of Ap-CH and Pf-FR depict plasmid and phage regions. Heatmap displays the composition of phage-regions across scaffolds. Phylogenetic tree of p45 homologs. Scatterplots show differences in GC content and coverage between scaffolds.

Viral content in Ap-CH and Pf-FR. (A) Schematic representation of the genome assemblies of Ap-CH (top) and Pf-FR (bottom). Each assembly is represented as a circle accommodating the scaffolds. Black blocks indicate regions syntenic to Arsenophonus extrachromosomal elements. Other colored blocks represent phage regions (>1 kb) identified by Phaster. Inner ribbons connect syntenic blocks (>5 kb). (B) Composition of the phage regions. VP: number of viral proteins; HP: number of hypothetical non-viral proteins; APSE: number of APSE proteins. The barplot represents the size of each region in kb. (C) Maximum-likelihood phylogenetic tree of the p45 homologs, built with the model JTT + F + I + G4. Black circles on branches indicate >50% bootstrap support. The scale is given in substitutions per site. Strains are color-coded as in Fig. 1B. Polymerases from Citrobacter koseri (WP_200053203.1) and Salmonella enterica (EFS9905187.1) were used to root the initial tree. (D) Normalized long-read (LR) and short-read (SR) coverages for the scaffolds of Ap-CH (left) and Pf-FR (right). The color scale indicates the difference in GC content from the assembly average.