title: Comparative Genomic and Phylogenomic Analyses Reveal a Conserved Core Genome Shared by Estuarine and Oceanic Cyanopodoviruses.
abstract: Podoviruses are among the major viral groups that infect marine picocyanobacteria Prochlorococcus and Synechococcus. Here, we reported the genome sequences of five Synechococcus podoviruses isolated from the estuarine environment, and performed comparative genomic and phylogenomic analyses based on a total of 20 cyanopodovirus genomes. The genomes of all the known marine cyanopodoviruses are highly syntenic. A pan-genome of 349 clustered orthologous groups was determined, among which 15 were core genes. These core genes make up nearly half of each genome in length, reflecting the high level of genome conservation among this cyanophage type. The whole genome phylogenies based on concatenated core genes and gene content were highly consistent and confirmed the separation of two discrete marine cyanopodovirus clusters MPP-A and MPP-B. The genomes within cluster MPP-B grouped into subclusters mainly corresponding to Prochlorococcus or Synechococcus host types. Auxiliary metabolic genes tend to occur in a specific phylogenetic group of these cyanopodoviruses. All the MPP-B phages analyzed here encode the photosynthesis gene psbA, which are absent in all the MPP-A genomes thus far. Interestingly, all the MPP-B and two MPP-A Synechococcus podoviruses encode the thymidylate synthase gene thyX, while at the same genome locus all the MPP-B Prochlorococcus podoviruses encode the transaldolase gene talC. Both genes are hypothesized to have the potential to facilitate the biosynthesis of deoxynucleotide for phage replication. Inheritance of specific functional genes could be important to the evolution and ecological fitness of certain cyanophage genotypes. Our analyses demonstrate that cyanopodoviruses of estuarine and oceanic origins share a conserved core genome and suggest that accessory genes may be related to environmental adaptation.
authors.affiliation: CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China.
authors.forename: Sijun
authors.initials: S
authors.lastname: Huang
authors.affiliation: CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China.
authors.forename: Si
authors.initials: S
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China.
authors.forename: Nianzhi
authors.initials: N
authors.lastname: Jiao
authors.affiliation: Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America.
authors.forename: Feng
authors.initials: F
authors.lastname: Chen
mesh_terms: D059001:Aquatic Organisms / Q000235:genetics; D001435:Bacteriophages / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D000458:Cyanobacteria / Q000235:genetics; D063366:Estuaries; D005814:Genes, Viral; D016679:Genome, Viral; D023281:Genomics / Q000379:methods*; D016013:Likelihood Functions; D009792:Oceans and Seas; D010802:Phylogeny; D017902:Podoviridae / Q000235:genetics*; D014764:Viral Proteins / Q000235:genetics
chemical_list: D014764:Viral Proteins