Exploratory analysis of Symbiodinium transcriptomes reveals potential latent infection by large dsDNA viruses

<jats:title>Summary</jats:title><jats:p>Coral reefs are in decline worldwide. Much of this decline is attributable to mass coral bleaching events and disease outbreaks, both of which are linked to anthropogenic climate change. Despite increased research effort, much remains unknown about these phenomena, especially the causative agents of many coral diseases. In particular, coral‐associated viruses have received little attention, and their potential roles in coral diseases are largely unknown. Previous microscopy studies have produced evidence of viral infections in <jats:italic>Symbiodinium</jats:italic>, the endosymbiotic algae critical for coral survival, and more recently molecular evidence of <jats:italic>Symbiodinium</jats:italic>‐infecting viruses has emerged from metagenomic studies of corals. Here, we took an exploratory whole‐transcriptome approach to virus gene discovery in three different <jats:italic>Symbiodinium</jats:italic> cultures. An array of virus‐like genes was found in each of the transcriptomes, with the majority apparently belonging to the nucleocytoplasmic large DNA viruses. Upregulation of virus‐like gene expression following stress experiments indicated that <jats:italic>Symbiodinium</jats:italic> cells may host latent or persistent viral infections that are induced via stress. This was supported by analysis of host gene expression, which showed changes consistent with viral infection after exposure to stress. If these results can be replicated in <jats:italic>Symbiodinium</jats:italic> cells <jats:italic>in hospite</jats:italic>, they could help to explain the breakdown of the coral‐<jats:italic>Symbiodinium</jats:italic> symbiosis, and possibly some of the numerous coral diseases that have yet to be assigned a causative agent.</jats:p>