Endogenous giant viruses contribute to intraspecies genomic variability in the model green alga Chlamydomonas reinhardtii

Abstract

Chlamydomonas reinhardtii is an important eukaryotic alga that has been studied as a model organism for decades. Despite extensive history as a model system, phylogenetic and genetic characteristics of viruses infecting this alga have remained elusive. We analyzed high-throughput genome sequence data of numerous C. reinhardtii isolates, and in six strains we discovered endogenous genomes of giant viruses reaching over several hundred kilobases in length. In addition, we have also discovered the entire genome of a closely related giant virus that is endogenized within the genome of Chlamydomonas incerta, one of the closest sequenced phylogenetic relatives of C. reinhardtii. Endogenous giant viruses add hundreds of new gene families to the host strains, highlighting their contribution to the pangenome dynamics and inter-strain genomic variability of C. reinhardtii. Our findings suggest that endogenization of giant viruses can have profound implications in shaping the population dynamics and ecology of protists in the environment.

Viral Complexity

“…The most striking example was found in Tetrabaena socialis , where two GEVEs with a total length of 3.2 Mbp were present, and over 10% of total ORFs in the genome could be traced back to giant viruses. Further, although the initial genome of the model green algae Chlamydomonas reinhardtii did not contain a GEVE, several of these elements were found in other strains of the same species, suggesting that GEVEs contribute to intraspecies genomic variability [ 191 ]. In addition to GEVEs, smaller remnants of endogenous giant viruses have been identified in various chlorophyte genomes [ 190 ].…”