Table 1.
Summary of marine cyanopodovirus genomes.
Fig 1.
Alignment of the 20 marine cyanopodovirus genomes.
Core genes are indicated by light blue arrows. The other arrows that are colored and linked by lines represent a few shared non-core genes with known or putative function. Abbreviation: MarR, MarR family transcriptional regulator; RNA pol, RNA polymerase; SSB, single-stranded DNA binding protein; endonuc., endonuclease; prim./hel., primase/helicase; DNA pol, DNA polymerase; exonuc., exonuclease; MazG, pyrophosphatase; RNR, ribonucleotide reductase; Hli, high light inducible protein; PsbA, photosystem II D1 protein; MCP, major capsid protein; ICP, internal core protein; TalC, transaldolase; ThyX, thymidylate synthase; HP, hypothetical protein.
Fig 2.
A and B. Pan- and core-genomes of cyanopodoviruses. The pan- (A) and core-genomes (B) were plotted as a function of the number of genomes analyzed. The pan-genome is the total number of genes of genomes in a subset sampled, while the core-genome is the genes shared by all genomes in the same subset. The line represents the average and the white box combing with dash lines represents estimated confidence interval. C and D. Fractions of core, accessory and unique genes of each genome.
Fig 3.
A. Linear relationship between the average protein sequence identity of core genes and the fraction of shared genes between two genomes. B. Multidimensional scaling showed the topological distances among the phylogenetic trees for core genes. The dash circle surrounds a relative more conserved core. Abbreviations refer to the legend of Fig 1.
Fig 4.
Whole genome phylogenies and network of cyanopodoviruses.
A, a phylogenetic tree based on the concatenated core genes built by using the distance method; B, a consensus tree inferred from ML trees built for the 15 core genes; C, a dendrogram built by using ML distance measurement based on gene content; D, a whole genome network constructed based on gene content. Synechococcus podoviruses were shown in blue and Prochlorococcus podoviruses shown in green. Black, grey and open circles respectively represent bootstrap supports of 100%, 75–99% and 50–74%. The grey shading in panel A indicates cluster MPP-A and subclusters MPP-B1, B2, B3 and B4, and those cluster/subclusters that exist in panel B and C are also marked with shading.
Fig 5.
Distribution pattern of accessory genes (n = 99) among the 20 marine cyanopodovirus genomes.
A black box represents a presence. Cyano_T7_GC stands for T7-like cyanophage gene cluster. The dendrograms were created based on the presence/absence matrix of accessory genes. The UPGMA and WPGMA methods were used to cluster the genes and the phages, respectively. The right column lists those genes with known/putative functions. Red boxes (A-H) indicate genes which were enriched or absent in certain phage groups. All the 349 COGs found among the 20 genomes were listed in S1 File.
Fig 6.
Maximum likelihood phylogenetic analysis of thymidylate synthase gene thyX in cyanophages and cyanobacteria.
Cyanobacterial and cyanophage sequences were shown in color and other bacterial and viral sequences in black. Bootstrap test values higher than 75% were shown.