Yikes. This year has been a doozy, and while we all know that the hand on the wall (if you have one of those old fashioned things) that strikes midnight on December 31st will not put out the dumpster fires that we are living amongst, we can hope that 2021 will (maybe….possibly) bring something good… yes, I’m knocking on wood.
I know I’m not alone, but I’ve recently heard a bunch about viruses. Maybe it’s fitting to end this chapter of what has turned out to be a completely wild year, by learning even more about viruses…of the giant variety.
As it turns out, viruses are everywhere and an important way for DNA to get shuffled around. As a side note, there is a ton we don’t know about how DNA moves between and among genomes, and if you’re interested in this kind of stuff, check out this preprint regarding a proposed new class of mobile genetic elements identified in the marine cyanobacterium Prochlorococcus.
Anyway, back to the giant viruses, the authors of a cool study out last month put it succinctly:
“Endogenous viral elements (EVEs) – viruses that have integrated their genomes into those of their hosts – are prevalent in eukaryotes and have an important role in genome evolution.”– Moniruzzaman et al., 2020
Moniruzzaman and colleagues focus on EVEs that are HUGE (think hundreds of kb), and originate from what are commonly called ‘giant viruses’, aka nucleocytoplasmic large DNA viruses (NCLDVs). These are actually the biggest viruses yet characterized, which already makes them interesting. It’s not shocking that like so many things out there, they are not completely understood. The authors decided to focus on studying NCLDVs in the phylum Chlorophyta.
The authors chose 65 genomes from the Chlorophyta (a diverse group of green algae that are closely related to plants) that were already available, and in over a third of these they found evidence of giant NCLDVs. Ultimately, they identified 18 giant EVEs (GEVEs) that ranged from 78 to 1,925 kb in size in a total of 12 of the genomes studied.
This is pretty cool. To start, the identified GEVEs had between 76 and 1,782 predicted genes, that’s quite a few viral genes encoded in those eukaryotic genomes. The GEVEs also have a higher coding density than the rest of the genome, so even if they might not seem like huge chunks of DNA, they can make up a disproportionately large chunk of the coding potential in a genome. While the authors were able to trace these GEVEs in most cases to single viruses, there was also evidence of duplications and gene loss, so there had been some shuffling around in the genome post GEVEs acquisition, indicating that these are dynamic regions of the genome. The study also found introns in multiple GEVE genes, matching previous findings that horizontally acquired genes acquire introns. Along with a suite of other convincing evidence, the authors conclude that “GEVEs represent bona fide components of algal genomes.” However, the question remained regarding the history of where these GEVEs really came from.
The authors wanted to understand if the GEVEs were from different distinct integration events of a virus into the genomes, or if there was one event that happened that was then passed along throughout speciation within the Chlorophyta. They were able to determine that there were indeed multiple events since these GEVEs came from multiple viruses of different phylogenies and that they did not consistently have evidence for co-diversification within the host genomes.
“The widespread endogenization of NCLDV into chlorophytes therefore represents an underappreciated aspect of eukaryotic genome evolution and suggests that many eukaryotic lineages have access to a much larger array of genomic material than previously thought.”Moniruzzaman et al., 2020
No matter which GEVEs you might ask (I’m so sorry), it is clear that the presence of these elements in chlorophyte genomes indicates how important they are to genome evolution. In fact, while not all of the genomes examined had clear GEVEs, there were proteins that matched reference NCLDVs in all 65 of the genomes included in the study.
There are many other examples of eukaryotic lineages (protists, metazoan, amoeba, and even moss) that harbor evidence of NCLDV genes and this is just another cool step towards unraveling more about genome evolution.
Moniruzzaman, M., Weinheimer, A.R., Martinez-Gutierrez, C.A. and Aylward, F.O., 2020. Widespread endogenization of giant viruses shapes genomes of green algae. Nature, pp.1-5.