Raw whole genome amplification and amplification-free shotgun metagenomic data of Symbiomonas scintillans cells and cultures. Symbiomonas scintillans

Symbiomonas scintillans Guillou et Chretiennot-Dinet, 1999 is a small (1.4 micron) heterotrophic bikosian stramenopile. The genus was named based on the presence of endosymbiotic bacteria in its endoplasmic reticulum, however, like most such endosymbionts neither the identity nor functional association with its host were known. We generated both amplification-free shotgun metagenomics and whole genome amplifcation sequencing data from S. scintillans strain RCC257, but were unable to detect any sequences from known lineages of endosymbiotic bacteria. Instead, several scaffolds with deep coverage in our assembly were closely related to prasinoviruses infecting the green algae Ostreococcus lucimarinus, Bathycoccus prasino, and Micromonas pusilla (OlV, BpV, and MpV, respectively). Using the BpV genome as a reference, we assembled one near-complete 190 kbp draft genome encoding all hallmark prasinovirus genes, as well as two additional highly fragmented assemblies of closely related but distinct viruses. Similar draft viral genomes were also obtained from another S. scintillans strain, RCC24, altogether suggesting S. scintillans is infected with multiple giant viruses (SsVs). A multi-gene tree showed the SsV genomes formed a highly supported clade that was sister to BpV2, OlVs, and MpVs. Transmission electron microscopy also revealed a 190 nm virus-like particle congruent with the morphology and size of the endosymbiont originally reported in S. scintillans. These data underscore just how little we currently understand most endosymbiotic associations: this case initially appeared to be an obligate intracellular bacteria, but is instead a virus.