Marine Prasinovirus Genomes Show Low Evolutionary Divergence and Acquisition of Protein Metabolism Genes by Horizontal Gene Transfer

Although marine picophytoplankton are at the base of the global food chain, accounting for half of the planetary primary production, they are outnumbered 10 to 1 and are largely controlled by hugely diverse populations of viruses. Eukaryotic microalgae form a ubiquitous and particularly dynamic fraction of such plankton, with environmental clone libraries from coastal regions sometimes being dominated by one or more of the three genera Bathycoccus, Micromonas, and Ostreococcus (class Prasinophyceae). The complete sequences of two double-stranded (dsDNA) Bathycoccus, one dsDNA Micromonas, and one new dsDNA Ostreococcus virus genomes are described. Genome comparison of these giant viruses revealed a high degree of conservation, both for orthologous genes and for synteny, except for one 36-kb inversion in the Ostreococcus lucimarinus virus and two very large predicted proteins in Bathycoccus prasinos viruses. These viruses encode a gene repertoire of certain amino acid biosynthesis pathways never previously observed in viruses that are likely to have been acquired from lateral gene transfer from their host or from bacteria. Pairwise comparisons of whole genomes using all coding sequences with homologous counterparts, either between viruses or between their corresponding hosts, revealed that the evolutionary divergences between viruses are lower than those between their hosts, suggesting either multiple recent host transfers or lower viral evolution rates.Phytoplankton is responsible for about half of the photosynthetic activity of the planet (13), with the other half being ensured by terrestrial plants. Phytoplankton is essentially composed of unicellular organisms which have a high turnover rate, and whereas terrestrial plants are renewed on average once every 9 years, the global phytoplankton population is replaced approximately every week (13). Although the ecological importance of viruses has previously been debated, they are now recognized as major players in regulating these highly dynamic phytoplankton populations. Indeed, viruses are the most numerous biological entities in the ocean, infecting all marine organisms from prokaryotes to uni- and multicellular eukaryotes (36). Cell death following viral infection produces particulate and dissolved organic matter that in turn fuels the growth of other phytoplankton. The importance of this viral shunt is not yet well understood although some studies suggest that it constitutes an important flux that must be taken into account in marine trophic transfer models.Among viruses affecting the eukaryotic phytoplankton, several large double-stranded DNA (dsDNA) viruses have been described, and these viruses have been named phycodnaviruses because they infect algae (12). However, the term “alga” has no evolutionary significance, and phycodnaviruses infect phylogenetically distantly related organisms. Thus, comparisons of dsDNA viruses infecting organisms as diverse as haptophytes, dinoflagellates, and green algae likely span the same order of evolutionary distances as comparisons of viruses of animals with those of plants. In order to understand the evolution of these viruses, comparisons between more closely related host-virus combinations are desirable and are even more valuable if DNA sequence information about their host species'' genomes is available. Viruses infecting Chlorophyta, which include most green algae, thus present attractive systems for such analyses. In this phylum, both prasinoviruses and chloroviruses, infecting Prasinophyceae and Trebouxiophyceae, respectively, have been described.Several dsDNA viruses have been described infecting different Chlorella sp. unicellular green algae (Trebouxiophyceae), which are symbionts of the ciliate Paramecium bursaria (14, 15, 44) or of the heliozoon Acanthocystis turfacea (16). They belong to the nucleocytoplasmic large DNA viruses (NCLDV), indicating that they either replicate exclusively in the cytoplasm of the host cell or start their life cycle in the host nucleus but complete it in the cytoplasm (20, 46). NCLDV can also infect members of the Prasinophyceae, an ecologically important class of microalgae that are found in all oceans (39). Prasinophyceae can dominate the eukaryotic picoplankton fraction in coastal areas, and a high proportion of the DNA sequences in many environmental DNA clone libraries can be attributed to one or more of the three genera Bathycoccus, Micromonas, and Ostreococcus (31, 42). Two dsDNA Ostreococcus viruses have been sequenced (9, 40), but no viruses specific to Bathycoccus have yet been reported (2, 6). Both dsDNA and RNA Micromonas viruses have been described although information about their genomes is not yet available (5, 8). Phylogenetic analyses based on their DNA polymerase or major capsid gene sequences suggest that chloroviruses and prasinoviruses form a monophyletic group (4). Since host genomes of two Chlorella species and three Prasinophyceae genera are available, the possibility of horizontal gene transfer (HGT) between hosts and their viruses can be investigated and might provide key insights into their coevolution. Both chloroviruses and prasinoviruses have a DNA polymerase gene but no DNA-dependent RNA polymerase, in contrast to the Emiliania huxleyi virus EhV-86 (41), which is consistent with a large evolutionary divergence between these viruses.Here, we describe the complete sequences of two dsDNA Bathycoccus virus genomes, one dsDNA Micromonas virus genome, and one new dsDNA Ostreococcus virus genome. Comparison between them revealed a high degree of conservation, both for orthologous genes and for synteny. Several specific pathways, such as amino acid biosynthesis, are encoded differentially by genes never previously identified before in viruses, and we compared these genomes with those of the six available Chlorella viruses. We propose a new phylogeny to reconcile the wide evolutionary distances between phycodnavirus genomes with those of their hosts.