DOI: 10.6084/m9.figshare.29299352.v3
title: <b>Expanding diversity of virome associated with ammonium-oxidizing archaea and related lineages</b>

description: The supplementary datasets and extended data of "Expanding diversity of virome associated with ammonium-oxidizing archaea and related lineages" (https://www.biorxiv.org/content/10.1101/2025.08.23.671958v2):<br>Supplementary DatasetDataset 1. The metagenomic assembled contigs used in this study were derived from public databases, encompassing metagenomes originating from four types of extreme environments: acidic, deep sea, hydrothermal, and sea ice habitats. The associated metadata includes study names, IMG accession numbers, accessible URLs, and corresponding publications.Dataset 2. The metadata of Nitrososphaeria-associated virus and mobile genetic element (MGE) contigs. This table encompasses contig IDs, associated metagenome/genome identifiers, geographic information, related research project names, taxonomic information, viral classifier confidence scores, genomic features, data source, environmental origin details, host information, and the proportion of shared genes between each virus (or MGE) and archaeal lineages.Dataset 3. Genome-content similarity between Nitrososphaeria-associated virus and mobile genetic element (MGE) contigs and other reference viral genomes.Dataset 4. Functional annotation of proteins encoded by Nitrososphaeria-associated viruses and mobile genetic elements (MGEs). This table includes the IDs of Nitrososphaeria-associated viruses and MGEs, family-level taxonomic information, viral cluster assignments generated by vConTACT2, contig lengths, putative morphotype information, archaeal lineage information, environmental context, protein IDs, functional domain accession numbers, functional domain annotations, viral auxiliary gene labels and corresponding database names.Dataset 5. Sharing of CRISPR spacer sequences among archaeal genomes. This table includes genome IDs of the paired archaeal genomes, their taxonomic information, and the viral or mobile genetic element (MGE) contigs targeted by the corresponding spacers.Dataset 6. Horizontal gene transfer (HGT) events between viruses or mobile genetic elements (MGEs) and their associated archaeal lineages. This table includes open reading frame (ORF) pairs derived from viruses or MGEs and archaea, the inferred direction of transfer, taxonomic information of both archaeal and associated viral lineages, functional annotations and accession numbers, enzymatic reaction equations, and metabolic functional classifications across three distinct aspects.Dataset 7. CRISPR cassettes identified in the archaeal genomes involved in this study were typed using CRISPR-Cas-Identifier. This table summarizes the results generated by CRISPR-Cas-Identifier, including archaeal genome IDs, cassette types, cassette coordinates, and the associated Cas-related proteins.Dataset 8. Performance of viral recall by three different viral identification pipelines based on a test set of viruses or mobile genetic elements (MGEs). VS2 and DVF denote VirSorter2 and DeepVirFinder, respectively.Dataset 9. Scoring matrix for identifying horizontal gene transfer (HGT) events based on the approach proposed by Irwin et al. Specifically, potential HGTs are quantitatively evaluated across four distinct criteria: transfer conditions (cross-lineage or intra-lineage), G+C content, scaffold N50, and the taxonomic information of the open reading frames (ORFs) flanking the candidate HGT region.<br>Extended DataData 1. The genome diagram and functional annotation of representative genomes from ten newly established viral families. Boxes denote individual open reading frames (ORFs), with the colour gradient indicating the sharing rate of each ORF among members within the family. ORFs with a sharing rate greater than 0.9 are considered to encode viral hallmark proteins (VHPs), which are indicated by asterisks above the corresponding ORFs.Data 2. The Bayesian and Maximum-likelihood tree of major capsid proteins encoded by Nitrososphaeria-associated viruses and mobile genetic elements.Data 3. The Bayesian and Maximum-likelihood tree of terminase proteins encoded by Nitrososphaeria-associated viruses and mobile genetic elements.Data 4 The structural predication of HK97-like capsid proteins from AlphaFold2.Data 5. The structural predication of SIRV2-like capsid proteins from AlphaFold2.Data 6. The Maximum-likelihood tree of proteins that were potentially involved in horizontal gene transfers (HGTs). These trees were used to determine HGT events based on their topologies.Data 7. The Nitrososphaeria-associated CRISPR spacers sequences, which were predicted from MinCED and CRASS.Data 8. The Maximum-likelihood tree of UbiG and ArsR proteins encoded by Nitrososphaeria-associated viruses and cellular organisms.<br>