Cryptic infection of a giant virus in a unicellular green alga.

Abstract

Latency is a common strategy in a wide range of viral lineages, but its prevalence in giant viruses remains unknown. In this work, we describe a 617-kilo-base pairs integrated giant viral element in the model green alga <i>Chlamydomonas reinhardtii</i>. We resolved the integrated viral genome using long-read sequencing, identified a putative polintovirus-like integrase, and show that viral particles accumulate primarily during the stationary growth phase. A diverse array of viral-encoded selfish genetic elements is expressed during viral activity, including several Fanzor nuclease-encoding transposable elements. In addition, we show that field isolates of <i>Chlamydomonas</i> spp. harbor signatures of endogenous giant viruses related to the <i>C. reinhardtii</i> virus that exhibit similar infection dynamics, suggesting that giant virus latency is prevalent in natural host communities. Our work describes an unusually large temperate virus of a unicellular eukaryote, substantially expanding the scope of cryptic viral infections in the virosphere.