The sequencing and annotation of two bacteriophages isolated from the cyanobacterium Acaryochloris

Marine cyanobacteria (blue green algae) are responsible for approximately one-quarter of global carbon fixation, thereby mitigating the effects of human carbon dioxide emissions. One of the main factors that controls the evolution and population genetics of cyanobacteria is cyanophages. The five completely sequenced cyanophage genomes have shown that the biology of the two organisms is tightly interlinked. Amazingly phages have picked up parts of the cyanobacterial genome, which they use to their advantage during infection, altering the host physiology. Only phages from two genera of cyanobacteria have been fully sequenced (Synechococcus and Prochlorococcus). We currently have little idea if all cyanophages have picked up host genes and if so when these events occurred. In order to understand this it is necessary to look at other cyanophage genomes to see if they show the same traits. Cyanophage are difficult to isolate and to work with but I have isolated two bacteriophages from the closest known relative of these two genera; Acaryochloris. I propose a programme of research to sequence and annotate the genome these two phages. This research programme is exciting in a number of ways. The cyanobacterial host Acaryochloris is intriguing in that it is the only organism to photosynthesise using chlorophyll d rather than chlorophyll a. It also has a unique arrangement of accessory pigments. The possession of chlorophyll d means that it can absorb light in the far red end of the spectrum which appears to allow the organism to be able to live in much darker environments, hence it has been found associated with sea squirts (Ascidia) and growing on the underside of red algae. We will compare the genome content of the phages with its cyanobacterial host (this is in the final stages of being sequenced and will be finished before the phage sequencing project is initiated). This will allow us to see if phages in this system have contributed to the evolution and potentially to the functioning of photosynthesis in Acaryochloris. The bacteriophages I am proposing to sequence were scraped from the outside sea squirts. Thus they are the first cyanophages to be isolated from a symbiotic cyanobacterium and the first to have been isolated from an invertebrate. An analysis of the genomes of these phages may reveal genes which benefit the symbiotic nature of the cyanobacteria. As the cyanobacterium is also thought to grow inside the sea squirts, they may even contain genes from the invertebrate. The sequencing of these Acaryochloris phage genomes may hold the key to understanding several fundamental aspects of cyanophage evolution and evolution in general.