DOI: 10.6084/m9.figshare.29646311
title: Supplementary_data.tar.gz

description: The supplementary material contains the following data :<br>(i) Data corresponding to the Results section ‘Novel ECVs further extend the ancestral host range of the <i>Caulimoviridae</i>’:<b>RT_aa.fa</b>: This fasta file comprises 369 amino acid sequences corresponding to the RT domain, including 261 newly detected ECRTs (headers: number_TagPlant), 2 RTs from TSA data (headers: TSA_TagPlant), 98 RTs from public data (headers: REF_RT_virusName), and 8 RTs from <i>Ortervirales</i> (headers: REF_RT_OUTGP)<b>RT_aa_network_guidance_098.aln</b>: Alignment file of RT_aa.fa performed with guidance. This alignment was used to build the phylogenetic network that guided the cutoff selection of the OTU clustering<br>(ii) Data corresponding to the Results section ‘Phylogenetic analysis’:<b>RT_RH_nt_Caulimoviridae.fa</b>: This fasta file comprises 143 nucleotide sequences corresponding to the RT-RH domain, including 73 reference sequences, 69 novel sequences (headers: OTU_number|sequence_id), and the outgroup Ty3.<b>RT_RH_nt_Caulimoviridae.aln</b>: Alignment with Mafft of the sequences from RT_RH_nt_Caulimoviridae.fa<b>Caulimoviridae_Bayesian_phylogeny.nexus </b>and <b>Caulimoviridae_MaximumLikelihood_phylogeny.nexus: </b>The two phylogenetic trees built with Bayesian and Maximum likelihood methods, respectively, from RT_RH_nt_Caulimoviridae.aln.<br>(iii) Data corresponding to the Results section ‘Characterization of Caulimovirid Clade C’:<b>RT_aa_Ortervirales.fa</b>: This fasta file comprises 52 amino acid sequences corresponding to the RT domains, including 28 <i>Ortervirales</i> sequences from the Gypsy database (Llorens <i>et al</i>. 2011) belonging to the families <i>Belpaoviridae</i>, <i>Pseudoviridae</i>, <i>Retroviridae</i>, and <i>Metaviridae</i>, and 24 <i>Caulimoviridae</i> sequences.<b>RT_aa_Ortervirales.aln</b>: An alignment file built with Mafft from RT_aa_Ortervirales.fa.<b>RT_aa_Ortervirales.nwk</b>: A phylogenetic tree built with maximum likelihood method from RT_aa_Ortervirales.aln.<b>30K_MP.fa</b>: This fasta file comprises 332 amino acid sequences corresponding to the movement protein domains, including 286 sequences from Butkovic <i>et al.</i> (2024), representing the following plant viral families: <i>Alphaflexiviridae</i>, <i>Aspiviridae</i>, <i>Betaflexiviridae</i>, <i>Bromoviridae</i>, <i>Botourmiaviridae</i>, <i>Caulimoviridae</i>, <i>Fimoviridae</i>, <i>Geminiviridae</i>, <i>Kitaviridae</i>, <i>Mayoviridae</i>, <i>Phenuiviridae</i>, <i>Rhabdoviridae</i>, <i>Secoviridae</i>, <i>Tospoviridae,</i> and <i>Virgaviridae</i>, as well as 46 <i>Caulimoviridae</i> sequences identified using Caulifinder.<b>30K_MP_trimed05.aln: </b>An alignment file built with Mafft from 30K_MP.fa.<b>30K_MP_maximum_likelihood</b>: A phylogenetic tree built with the maximum likelihood method from 30K_MP_trimed05.aln<b>.</b><b>WolV1.docx: </b>This file contains the sequences of the genome and the 2 ORFs of Wollendovirus1.<br>(iv) Data corresponding to the Results section ‘Evidence of patterns of cospeciation’:<b>Agathis_dammara_OTU19_RT_contig.fa</b>: This file contains the contig built from the DNA short-read sequences of <i>Agathis dammara</i>. This contig encodes a caulimovirid RT domain.<br><b>Licence</b>: CC BY-NC 4.0 (NON COMMERCIAL USE ONLY) <br>