Giant viruses, so named because they tend to be about 10 times larger than the average virus, have challenged traditional ideas in virology since their discovery in 2003. In addition to their unusually large size, their genomes sometimes include genetic contributions from bacteria and eukaryotes, including metabolic genes. Because of this, “they don’t necessarily look viral” at the genomic level, says Frank Aylward, a virologist at Virginia Tech and a co-author of the study.

Towards the beginning of his postdoc in Aylward’s lab, Mohammad “Monir” Moniruzzaman went searching for a handful of giant virus marker genes in all genomes accessible through the National Center for Biotechnology Information’s many databases—an exploratory exercise to see what came back. While most of the genes appeared in genomes labelled as viruses, Moniruzzaman says he was surprised by how many of these giant virus genes appeared in genomes labelled as belonging to microscopic marine phytoplankton.

Aylward and Moniruzzaman first thought they might be picking up contamination. But when they looked more closely, they noticed genetic signals suggesting parts of the viruses had been incorporated into the genomes of their hosts. Following up on this hypothesis, the team went looking for systematic evidence of this integration in 65 publicly available green algae genomes, some of which are known to be hosts to giant viruses.

The giant virus Ostreococcus tauri virus (OtV-1) can insert large portions of its roughly 200,000 base pair genome into the genome of its host Ostreococcus tauri, the smallest known free-living eukaryote. The arrow points to the attachment site for host cell absorption.

Moniruzzaman and his colleagues developed a bioinformatics tool, called Viral Recall, to identify regions in algal genomes suspected of having a viral origin based on several cues. For example, they used the tool to scan for certain viral hallmark genes, clear demarcations between the two genomes, shared genes between virus and host, and the presence of noncoding introns and large duplications within the integrated viral sequences thought to be caused by the host’s molecular machinery.

The researchers identified 18 examples of “giant endogenous viral elements” (GEVEs) within a dozen host genomes, meaning that some hosts had more than one of these GEVEs integrated into their genetic code. In some cases, the viral contributions were fragmented, representing only a small fraction of the virus genome. But in two samples, the entire viral genome appears to have made the jump into the phytoplankton, making up as much as 10 percent of the host’s genes. Overall, these GEVEs contributed between 78 and 1,782 genes. 

“This essentially opens up a large conduit of horizontal gene transfer from viruses into eukaryotes,” Aylward says. “All sorts of possibilities open up once you see these huge cases of endogenization.” 

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