Phylogenetic signal retention across evolutionary depths in highly divergent mitovirus RNA-dependent RNA polymerases

Abstract

This file contains the comprehensive dataset used in this study, comprising 1,036 mitovirus and mitovirus‑like sequences in FASTA format. The dataset includes all mitovirus species currently recognized by the Mitoviridae Study Group of the International Committee on Taxonomy of Viruses (International Committee on Taxonomy of Viruses Mitoviridae Study Group. (2021). ICTV taxonomy release: Executive Committee 53, Proposal 2021.003F. Retrieved December 12, 2025, from https://talk.ictvonline.org/taxonomy/), comprising 46 members of the genus Unuamitovirus, 47 of Duamitovirus, 9 of Triamitovirus, and 1 of Kvaramitovirus. In addition, recently described and proposed mitovirus lineages were incorporated for comparative phylogenetic purposes, including 10 novel putative members of the genus Kvaramitovirus (Jacquat et al., 2023, DOI: 10.3390/v15020340; Jacquat et al., 2024,DOI: 10.1093/jeb/voae070), 19 putative animal-replicating mitoviruses designated as “Kvinmitovirus” (Jacquat et al., 2022, DOI: 10.1111/1462-2920.16202), 130 members of the proposed subfamily “Arkeomitovirinae” (Jacquat et al., 2023, DOI: 10.3390/v15020340), and 10 sequences tentatively classified as “large duamitoviruses” (Ezawa et al., 2023,DOI: 10.1128/mbio.00240-23). Furthermore, a comprehensive dataset comprising 763 putative mitovirus-derived RdRp amino acid sequences—including both nearly complete and partial sequences—reported by Begeman et al. (2023,DOI: 10.1128/msystems.01002-22), was incorporated into the analysis. In that study, raw reads from diverse metagenomic and metatranscriptomic datasets spanning multiple geographic regions and ecological environments were reassembled and subjected to functional annotation and phylogenetic analyses. Classification of these sequences as mitovirus-like RdRps was based on explicit and objective selection criteria integrating phylogenetic placement with advanced similarity-based approaches, rather than on host association or genome context. The 763 amino acid sequences (Table S2 in Begeman et al., 2023; mSystems.01002-22-s0002) were retrieved in FASTA format from the protein column, with sequence headers corresponding to the descriptions provided in the nodes column of the same supplementary table. Aditionally, it include five outgroup sequences: the RNA replicase beta subunit of Escherichia phage Qβ (NCBI: NP_046752.1); the putative RNA replicase beta subunit of Enterobacteria phage GA (CAA27499.1); the RNA‑directed RNA polymerase of ssRNA phage SRR6960799_27 (DAD50689.1); and the RdRps of Saccharomyces 20S and 23S RNA narnaviruses (NP_660178.1 and NP_660177.1, respectively).