Resolving deep evolutionary relationships within the RNA virus phylum Lenarviricota

Abstract

The RNA virus phylum Lenarviricota is comprised of the fungi-associated families Narnaviridae and Mitoviridae, the RNA bacteriophage Leviviridae, and the plant and fungi-associated Botourmiaviridae. Members of the Lenarviricota are abundant in most environments and boast remarkable phylogenetic and genomic diversity. As this phylum includes both RNA bacteriophage and fungi-and plant-associated species, the Lenarviricota likely mark a major evolutionary transition between those RNA viruses associated with prokaryotes and eukaryotes. Despite the remarkable expansion of this phylum following metagenomic studies, the phylogenetic relationships among the families within the Lenarviricota remain uncertain. Utilising a large data set of relevant viral sequences, we performed phylogenetic and genomic analyses to resolve the complex evolutionary history within this phylum and identify patterns in the evolution of virus genome organisation. Despite limitations reflecting very high levels of sequence diversity, our phylogenetic analyses suggests that the Leviviridae comprise the basal lineage within the Lenarviricota. Our phylogenetic results also support the construction of a new virus family – the Narliviridae – comprising a set of diverse and phylogenetically distinct species, including a number of uniquely encapsidated viruses. We propose a taxonomic restructuring within the Lenarviricota to better reflect the phylogenetic relationships documented here, with the Botourmiaviridae and Narliviridae combined into the order Ourlivirales, the Narnaviridae remaining in the order Wolframvirales, and these orders combined into the single class, the Amabiliviricetes. In sum, this study provides insights into the complex evolutionary relationships among the diverse families that make up the Lenarviricota.

Putative Mitoviruses without In-Frame UGA(W) Codons: Evolutionary Implications

“…This apparent inconsistency between members of the mitovirus genera was clarified in subsequent reconstructions, as described in the Section 3.7 , in which the monophyly of “Arkeomitovirinae”, formal mitoviruses, and mitoviruses genera were retained according to the ICTV report [ 20 ] and our previous study [ 21 ]. It should be remarked that the discrimination between mitoviruses, narnaviruses, narliviruses, botourmiaviruses and leviviruses shown in the present ML-trees ( Figure 2 and Figure S1 ) was consistent with the work of Sadiq and colleagues [ 41 ].…”

“…The obtained phylogenic tree showed three main clades whose phylogenetic relationships were consistent with a recent comprehensive phylogenetic study of the phylum Lenarviricota [ 41 ] ( Figure 2 ). Narnaviridae , Botourmiaviridae and “Narliviridae” form a sister clade to Mitoviridae , with “Leviviridae” being a basal group.…”

“…In addition to these searches, a data set of 8469 hypothetical proteins generated from 442 RNA sequencing libraries (NCBI BioProject accession code: PRJNA716119) reported by Sadiq et al [ 41 ] and Chen et al [ 42 ] were also inspected to be able to tentatively expand the number of members of the obtained clades “A” and “B”. These sequences were filtered to retain only hypothetical proteins with a Mitovirus RdRp CPD.…”

“…A deep evolutionary reconstruction including members of the “Narna-Levi” clade (formally phylum Lenarviricota ) was performed in order to assess the evolutionary relationships of the two new clades studied in the present work. It is worth mentioning that RNA replicases encoded by “Narna-Levi” viruses have a low overall similarity among the different taxonomic families which complicates the construction of a realistic tentative phylogenetic tree [ 41 , 43 ]. In particular, the aa sequences included in the present study ( Table S1 ) showed a global pairwise alignment identity of 27.91% (SD: 9.58%), indicating a technical limitation [ 44 ].…”

“…This evolutionary scenario also proposed that current cytoplasmatic narnaviruses emerged from ancient mitovirus-like naked replicons by a “jump” to the cytoplasm ( Figure 4 ). In light of new evidence, narnaviruses seemed to have evolved as a sister group to mitoviruses and gave rise to two other families of narna-like viruses: Botourmiaviridae and “Narliviridae” [ 41 ]. However, to simplify the discussion, we will only refer to the Narnaviridae family, which has evidence of sharing a common ancestor with mitoviruses.…”