Fig. 3

The phylogenetic analyses of cyanophages Pam1~Pam5. a Maximum-likelihood phylogenetic tree of TerL proteins from different phages indicates the putative DNA packaging mechanisms of Pam1~Pam5. Vertical lines cluster the phages that have similar DNA termini. The TerL sequences, except those of Pam1~Pam5, were classified as described previously [33, 67]. The bootstrap analysis was performed with 1000 repetitions, and the scale bar represents the number of substitutions per site. Cyanophages Pam1~Pam5 are highlighted in red. b The proteomic tree of Pam1~Pam5 against 148 previously reported cyanophages. The genome sequences of 19 freshwater cyanophages are colored in red. The four clusters are labeled in different colors: (I) marine Siphoviridae (blue), (II) freshwater cyanophages (yellow), (III) marine Autographiviridae (green), (IV) marine Myoviridae (pink). Pam1~Pam5 are marked with a red star, respectively. c, d Whole-genome alignments of c Pam2 against PA-SR01 (GenBank accession number: MT234670.1) and d Pam4 against S-2L (GenBank accession number: MW334946.1), respectively. The alignments were performed with the software Mauve [59]. Blocks with the same color indicate the homologous regions of two genomes, which are also connected by the same color lines. The height of the similarity profile corresponds to the sequence similarity, whereas regions outside the colored blocks indicate the lack of homology among the two genomes. The inverted blocks are indicated below the genome’s center axis (a horizontal line). The numbers above the alignments indicate the nucleotide positions in the genome