Identification of the Branching Order within the Kingdom Bamfordvirae

The kingdom Bamfordvirae comprises the majority of the realm Varidnaviria and, according to the 2021 release of Virus Taxonomy by the International Committee on Taxonomy of Viruses, consists of the phyla Nucleocytoviricota and Preplasmiviricota. There are several fundamental unresolved issues related to the evolution of Bamfordvirae. These are questions concerning Bamfordvirae taxonomy including the branching order of Nucleocytoviricota and the question of the monophyly of Preplasmiviricota. Here, based on the analyses of the individual core protein phylogenies, supertree, concatenated trees, dendrograms, as well as superdendrogram, we have refined the branching order of major groups within phylum Nucleocytoviricota using the rooting of the entire phylum on the cellular outgroups. These efforts resulted in several major changes in Bamfordvirae phylogeny. In particular, we showed that Nucleocytoviricota consists of two sister clades, consisting of Phycodnaviridae sensu lato on the one hand and Mimiviridae sensu lato, Iridoviridae/Ascoviridae, Marseilleviridae, pithoviruses including Cedratvirus, Solumvirus, Solivirus, and Orpheovirus, Mininucleoviridae, Asfarviridae sensu lato, and Poxviridae on the other hand. According to our data, Asfarviridae sensu lato and Poxviridae have likely originated from within the class Megaviricetes. We gave evidence for polyphyly of the phylum Preplasmiviricota and argued for a transfer of the families Lavidaviridae, Adintoviridae, and Adenoviridae from the phylum Preplasmiviricota into the phylum Nucleocytoviricota. We also argued for the origin of the Nucleocytoviricota from small prokaryotic viruses and gave arguments against the origin of Nucleocytoviricota from the Adintoviridae/Polinton-like viruses.