Comparative analysis of Actinobacteria phage-plasmids and their transduction potential

Mathematical Biology & Bioinformatics. 2023;18(2):323-346.

doi: 10.17537/2023.18.323.

• Figure S1. A complete pan-genome tree for Streptomyces phage Gilgamesh and phages containing homologs of its proteins. The scale bar represents the number of expected substitutions per site under the binary GTR2+FO+ASC+R4 substitution model. aBayes support/ultrafast bootstrap support are labelled.
• Figure S2.
• Figure S3
• Figure S4. A complete pan-genome tree for Streptomyces phage Gilgamesh and phages and plasmids containing the homologs of Gilgamesh proteins. The scale bar represents the number of expected substitutions per site under the binary GTR2+FO+ASC+R5 substitution model. aBayes support/ultrafast bootstrap support are labelled.
• Figure S5
• Figure S6
• Figure S7
• Figure S8. A complete phylogenomic tree for Streptomyces phage Gilgamesh and phages and plasmids containing homologs of its proteins. The tree constructed with the neighbor joining method from the pairwise distance matrix calculated for 572 sets of 10-mers. The scale bar shows the Sorensen distance as a percentage.
• Figure S9
• Figure S10. Phylogenetic tree inferred in IQ-TREE program from the alignment of the amino acid sequences of large terminase subunit. Ultrafast bootstrap support is labelled. The scale bar corresponds to the number of amino acid substitutions per site under PMB+F+R6 substitution model.
• Data S1. Clusters of phage homologs of Streptomyces phage Gilgamesh proteins obtained in GET_HOMOLOGUES
• Data S2. Clusters of phage and plasmid homologs of Streptomyces phage Gilgamesh proteins obtained in GET_HOMOLOGUES
• Table S1
• Table S2
• Table S3
• Table S4