Figure 1.
Features of the Prochlorococcus Podovirus P-SSP7
(A) Electron micrograph of negative-stained podovirus P-SSP7. Note the distinct T7-like capsid and tail structure. Scale bar indicates 100 nm.
(B) Genome arrangement of Prochlorococcus podovirus P-SSP7. The ORFs are sequentially numbered within the boxes, and gene names are designated above the boxes. Gene designations use T7 nomenclature for T7-like genes [24] or microbial nomenclature for non-phage genes. Class I, II, and III genes refer to those in T7 [66] that belong to gene regions primarily involved in host transcription of phage genes (class I), DNA replication (class II), and the formation of the virion structure (class III). The ORFs are designated by boxes, and in this genome, all ORFs are oriented in the same direction. Although the phage genome is one molecule of DNA, the representation is broken to fit on a single page. Note that the P-SSP7 genome is most similar to genomes of the T7-like phages.
(C) Taxonomy of best BLASTp hits for P-SSP7. Each predicted coding sequence from the phage genomes was used as a query against the nonredundant database to identify the taxon of the best hit (details in Materials and Methods). Blue slices indicate phage hits, while yellow slices indicate cellular hits.
(D) Diagrammatic representation of the genomic regions surrounding a putative phage and host integration site. This site consists of a 42-bp exact match between the podovirus P-SSP7 and its host Prochlorococcus MED4 located directly downstream of the phage integrase gene and the noncoding strand of a host tRNA gene.
Table 1.
Genome-Wide Characteristics of the Prochlorococcus Cyanophage P-SSP7 Relative to the Other Recognized Phage Groups within the Podoviridae [105]
Table 2.
Shared Genes in T7-Like Phages
Table 3.
Genome-Wide Characteristics of the Prochlorococcus Cyanomyophages P-SSM2 and P-SSM4 Relative to the Other Recognized Phage Groups within the Myoviridae [105]
Figure 2.
Electron Micrograph of Negative-Stained Prochlorococcus Myoviruses P-SSM2 and P-SSM4
Myovirus P-SSM2 with (A) non-contracted tail and (B) contracted tail, and myovirus P-SSM4 with (C) contracted tail and (D) non-contracted tail. Note the T4-like capsid, baseplate, and tail structure in both myoviruses. Scale bars indicate 100 nm.
Figure 3.
Genome Arrangement of the Prochlorococcus Myovirus P-SSM2
Gene names are designated above the box representing the ORF where genes were identified; descriptions of genes are in Table 4. The ORFs located above the centering line are on the forward DNA strand, whereas those below the line are on the reverse strand. Although the genome is one molecule, the representation is broken to fit the page. Colors indicate the putative role for the identified genes as inferred from T4 phage. Gene designations use T4 nomenclature for T4-like genes [104] or microbial nomenclature for non-phage genes.
Figure 4.
Genome Arrangement of the ProchlorococcusMyovirus P-SSM4
Gene nomenclature is as in Figure 3.
Figure 5.
Taxonomy of Best BLASTp Hits for P-SSM2 and P-SSM4
Each predicted coding sequence from both phage genomes was used as a query against the nonredundant database to identify the taxon of the best hit (details in Materials and Methods). Blue slices indicate phage hits, while yellow slices indicate cellular hits.
Table 4.
Shared Genes in T4-like Phages
Table 4.
Continued
Table 5.
Summary Table of Unique Features of Prochlorococcus Cyanophage Genomes That Are Uncommon among Known Phages
Figure 6.
Bioinformatically Identified Tail Fiber Genes from Prochlorococcus Myoviruses
Red bars indicate P-SSM2 ORFs (labeled as M2); blue bars indicate P-SSM4 ORFs (labeled as M4). Due to space constraints, P-SSM2 orf67 and P-SSM4 orf10 are broken as indicated.
Table 6.
Signature Cyanophage Genes?