Transcriptiome dynamics of cyanopodovirus S-SBP1 and its host Synechococcus sp. WH7803

Whole-genome expression dynamics of cyanopodovirus P-SSP7 and its host Prochlorococcus strain MED4 have been reported. To investigate whether cyanopodoviruses infecting Prochlorococcus and Synechococcus have similar transcription strategy and host response to phage infection, genomic and transcriptomic analyses were conducted on cyanopodovirus S-SBP1 that infects Synechococcus strain WH7803. S-SBP1 has a latent period of 8 h and a burst size of 30 progeny phages per cell. S-SBP1 was most similar to cyanopodovirus S-RIP2 that also infects Synechococcus WH7803, in terms of whole genome phylogenetic relationship and average nucleotide identity (ANI). Three hypervariable genomic islands were found when comparing the genomes of S-SBP1 and S-RIP2, and single nucleotide variants (SNV) were observed on three genes of S-SBP1, which are located within the island regions. Based on RNA-seq analysis, genes of S-SBP1 were clustered into three temporal express classes, with gene content within each class similar to that of P-SSP7. Thirty-two host genes were upregulated during phage infection, including those involved in carbon metabolism, ribosome component and stress response. These upregulated genes were also similar to those of Prochlorococcus MED4 in response to infection by P-SSP7. Our study demonstrates a programmed temporal expression pattern of cyanopodoviruses and hosts during infection. Overall design: Exponentially growing Synechococcus WH7803 culture was inoculated with phage S-SBP1 at a multiplicity of infection (MOI) of two. At the time points 15 min, 1 h, 3 h, 5 h and 7 h after phage lysate additon, cells from single treatment were collected for transcriptomic analysis. A parallel of control group without phage addition was also sampled at the time point of 30 min and 8 h. Seven RNA-seq libraries, which are five time points of phage addition treatment and two time points of control, were sequenced using the Illumina HiSeq platform.