A phylogenomic framework for charting the diversity and evolution of giant viruses

Abstract

Large DNA viruses of the phylum Nucleocytoviricota have recently emerged as important members of ecosystems around the globe that challenge traditional views of viral complexity. Numerous members of this phylum that cannot be classified within established families have recently been reported, and there is presently a strong need for a robust phylogenomic and taxonomic framework for these viruses. Here, we report a comprehensive phylogenomic analysis of the Nucleocytoviricota, present a set of giant virus orthologous groups (GVOGs) together with a benchmarked reference phylogeny, and delineate a hierarchical taxonomy within this phylum. We show that the majority of Nucleocytoviricota diversity can be partitioned into 6 orders, 32 families, and 344 genera, substantially expanding the number of currently recognized taxonomic ranks for these viruses. We integrate our results within a taxonomy that has been adopted for all viruses to establish a unifying framework for the study of Nucleocytoviricota diversity, evolution, and environmental distribution.

Viral histones: pickpocket’s prize or primordial progenitor?

“…Medusavirus represents a distinct family of NCLDVs in the order Pandoravirales [ 94 ] with a linear genome of 381 kb and an icosahedral capsid of approximately 260 nm with an internal membrane enclosing the DNA inside the capsid [ 29 ]. In culture, the virion is taken up by Acanthamoeba castellanii by phagocytosis, and once in the cytoplasm fuses with the nucleus where the virus replicates, in contrast to the cytoplasmic replication of Marseilleviridae .…”

“…Klosneuviruses, including indivirus and klosneuvirus KNV1, are related MAGs of 0.86 and 1.57 Mb, respectively, and form a distinct NCLDV clade within the mimiviruses [ 19 , 94 ]. Their hosts are believed to include cercozoan protists and ciliates [ 19 ].…”

“…The presence of highly divergent H4–H3-like and H2B–H2A-like doublets in the Pimascovirales [ 94 ] encompassing the Marseilleviridae, Iridoviridae , and Pithoviridae , and also in the Pandoravirales (medusavirus) and Imitervirales (mimivirus relatives), suggests that these proteins are vertically descended from a common viral ancestor rather than being independently captured from a proto-eukaryote. However, neighbor-joining trees present a more complicated picture (Fig.…”

Particle Morphology of Medusavirus Inside and Outside the Cells Reveals a New Maturation Process of Giant Viruses

“…Medusavirus is taxonomically classified in the phylum Nucleocytoviricota ( 7 ), which is traditionally referred to as the nucleocytoplasmic large DNA virus (NCLDV), an expansive group of double-stranded DNA (dsDNA) viruses that possess a large particle size encapsulating a large genome (>100 kb) and infect various eukaryotic hosts ( 8 , 9 ). The following families are classified in the phylum Nucleocytoviricota : Ascoviridae , Asfarviridae , Iridoviridae , Marseilleviridae , Mimiviridae , Phycodnaviridae , and Poxviridae ( 10 ).…”

Diversity of Giant Viruses Infecting Vermamoeba vermiformis

“…Although each giant virus encodes hundreds or thousands of distinct proteins, they share at the most only three universally conserved genes ( Colson and Raoult, 2010 ). A recent phylogeny-centered study proposed that phylum Nucleocytoviricota may be portioned in six orders comprising 32 families embracing all large DNA viruses including giant viruses ( Aylward et al, 2021 ).…”