Genomic Characterization of a Novel Freshwater Cyanophage Reveals a New Lineage of Cyanopodovirus

Abstract

Cyanobacteria are one of the dominant autotrophs in tropical freshwater communities, yet phages infecting them remain poorly characterized. Here we present the characterization of cyanophage S-SRP02, isolated from a tropical freshwater lake in Singapore, which infects Synechococcus sp. Strain SR-C1 isolated from the same lake. S-SRP02 represents a new evolutionary lineage of cyanophage. Out of 47 open reading frames (ORFs), only 20 ORFs share homology with genes encoding proteins of known function. There is lack of auxiliary metabolic genes which was commonly found as core genes in marine cyanopodoviruses. S-SRP02 also harbors unique structural genes highly divergent from other cultured phages. Phylogenetic analysis and viral proteomic tree further demonstrate the divergence of S-SRP02 from other sequenced phage isolates. Nonetheless, S-SRP02 shares synteny with phage genes of uncultured phages obtained from the Mediterranean Sea deep chlorophyll maximum fosmids, indicating the ecological importance of S-SRP02 and its related viruses. This is further supported by metagenomic mapping of environmental viral metagenomic reads onto the S-SRP02 genome.

Characterization of Three Novel Virulent Aeromonas Phages Provides Insights into the Diversity of the Autographiviridae Family

“…Furthermore, the Pelagibacter siphovirus Kolga [ 100 ] and more than 20 autographiviruses showed significant sequence identity over a DNA primase, ribonucleotide diphosphate reductase subunits, and a few small hypothetical proteins ( Figure S13 ). Moreover, two Synechococcus siphoviruses, KBS-S-2A [ 101 ] and S-CBS4 [ 102 ], were similar to Synechococcus autographiviruses S-SRP02 [ 103 ], S-B28 (NC_048171.1), and S-SRP01 [ 104 ] through a few hypothetical proteins ( Figure S14 ). It has not escaped our attention that the above-mentioned phages of the SG3 subgraph infect similar hosts, that is, marine bacteria of the Alphaproteobacteria class (often of the same taxonomic genus).…”

Biological and Genomic Characteristics of MaMV-DH01, a Novel Freshwater Myoviridae Cyanophage Strain

“…These results indicate that the burst size of a cyanophage is specific to individual phage strains, which may be related to their size. Surprisingly, the burst size of S-SRP02 determined by Zhang et al using quantitative PCR (qPCR) was estimated to be ~250 ( 30 ). This difference might arise from the different quantification methods used.…”

Synthesis and assembly of full-length cyanophage A-4L genome

“…Cyanophages, the viruses of blue-green algae, are abundant in aquatic ecosystem and play an important role in regulating the cyanobacteria biomass and community structure, which have been considered as a potential biological method for controlling the cyanobacterial bloom [ 11 ]. In recent years, a very limited number of freshwater cyanophages, compared to marine cyanophages, have been studied and most of them are highly host-specific while water blooms are usually caused by multiple cyanobacteria [ 12 ]. Refactoring and engineering artificial genomes can be obtained using synthetic biology strategies.…”