Supplementary_data.tar.gz
<p dir="ltr">The supplementary material contains the following data :</p><p><br></p><p dir="ltr">(i) Data corresponding to the Results section ‘Novel ECVs further extend the ancestral host range of the <i>Caulimoviridae</i>’:</p&...
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| مؤلفون آخرون: | , , , , , |
| منشور في: |
2025
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| _version_ | 1852018192779575296 |
|---|---|
| author | héléna vassilieff (19216723) |
| author2 | Saad Serfraz (21788297) Nathalie Choisne (11794232) Andrew D.W. Geering (21788291) Pierre Lefeuvre (21788302) Pierre-Yves Teycheney (21788305) Florian Maumus (21788294) |
| author2_role | author author author author author author |
| author_facet | héléna vassilieff (19216723) Saad Serfraz (21788297) Nathalie Choisne (11794232) Andrew D.W. Geering (21788291) Pierre Lefeuvre (21788302) Pierre-Yves Teycheney (21788305) Florian Maumus (21788294) |
| author_role | author |
| dc.creator.none.fl_str_mv | héléna vassilieff (19216723) Saad Serfraz (21788297) Nathalie Choisne (11794232) Andrew D.W. Geering (21788291) Pierre Lefeuvre (21788302) Pierre-Yves Teycheney (21788305) Florian Maumus (21788294) |
| dc.date.none.fl_str_mv | 2025-07-25T14:51:47Z |
| dc.identifier.none.fl_str_mv | 10.6084/m9.figshare.29646311.v1 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/dataset/Supplementary_data_tar_gz/29646311 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Molecular evolution Caulimoviridae endogenous virus Viral evolution |
| dc.title.none.fl_str_mv | Supplementary_data.tar.gz |
| dc.type.none.fl_str_mv | Dataset info:eu-repo/semantics/publishedVersion dataset |
| description | <p dir="ltr">The supplementary material contains the following data :</p><p><br></p><p dir="ltr">(i) Data corresponding to the Results section ‘Novel ECVs further extend the ancestral host range of the <i>Caulimoviridae</i>’:</p><ul><li><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)</li><li><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</li></ul><p><br></p><p dir="ltr">(ii) Data corresponding to the Results section ‘Phylogenetic analysis’:</p><ul><li><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.</li><li><b>RT_RH_nt_Caulimoviridae.aln</b>: Alignment with Mafft of the sequences from RT_RH_nt_Caulimoviridae.fa</li><li><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.</li></ul><p><br></p><p dir="ltr">(iii) Data corresponding to the Results section ‘Characterization of Caulimovirid Clade C’:</p><ul><li><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.</li><li><b>RT_aa_Ortervirales.aln</b>: An alignment file built with Mafft from RT_aa_Ortervirales.fa.</li><li><b>RT_aa_Ortervirales.nwk</b>: A phylogenetic tree built with maximum likelihood method from RT_aa_Ortervirales.aln.</li><li><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.</li><li><b>30K_MP_trimed05.aln: </b>An alignment file built with Mafft from 30K_MP.fa.</li><li><b>30K_MP_maximum_likelihood</b>: A phylogenetic tree built with the maximum likelihood method from 30K_MP_trimed05.aln<b>.</b></li><li><b>WolV1.docx: </b>This file contains the sequences of the genome and the 2 ORFs of Wollendovirus1.</li></ul><p><br></p><p dir="ltr">(iv) Data corresponding to the Results section ‘Evidence of patterns of cospeciation’:</p><ul><li><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.</li></ul><p><br></p><p dir="ltr"><b>Licence</b>: CC BY-NC 4.0 (NON COMMERCIAL USE ONLY) </p><p><br></p> |
| eu_rights_str_mv | openAccess |
| id | Manara_cc69080576fd8dfd7106fe77cdd8a07f |
| identifier_str_mv | 10.6084/m9.figshare.29646311.v1 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/29646311 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Supplementary_data.tar.gzhéléna vassilieff (19216723)Saad Serfraz (21788297)Nathalie Choisne (11794232)Andrew D.W. Geering (21788291)Pierre Lefeuvre (21788302)Pierre-Yves Teycheney (21788305)Florian Maumus (21788294)Molecular evolutionCaulimoviridaeendogenous virusViral evolution<p dir="ltr">The supplementary material contains the following data :</p><p><br></p><p dir="ltr">(i) Data corresponding to the Results section ‘Novel ECVs further extend the ancestral host range of the <i>Caulimoviridae</i>’:</p><ul><li><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)</li><li><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</li></ul><p><br></p><p dir="ltr">(ii) Data corresponding to the Results section ‘Phylogenetic analysis’:</p><ul><li><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.</li><li><b>RT_RH_nt_Caulimoviridae.aln</b>: Alignment with Mafft of the sequences from RT_RH_nt_Caulimoviridae.fa</li><li><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.</li></ul><p><br></p><p dir="ltr">(iii) Data corresponding to the Results section ‘Characterization of Caulimovirid Clade C’:</p><ul><li><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.</li><li><b>RT_aa_Ortervirales.aln</b>: An alignment file built with Mafft from RT_aa_Ortervirales.fa.</li><li><b>RT_aa_Ortervirales.nwk</b>: A phylogenetic tree built with maximum likelihood method from RT_aa_Ortervirales.aln.</li><li><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.</li><li><b>30K_MP_trimed05.aln: </b>An alignment file built with Mafft from 30K_MP.fa.</li><li><b>30K_MP_maximum_likelihood</b>: A phylogenetic tree built with the maximum likelihood method from 30K_MP_trimed05.aln<b>.</b></li><li><b>WolV1.docx: </b>This file contains the sequences of the genome and the 2 ORFs of Wollendovirus1.</li></ul><p><br></p><p dir="ltr">(iv) Data corresponding to the Results section ‘Evidence of patterns of cospeciation’:</p><ul><li><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.</li></ul><p><br></p><p dir="ltr"><b>Licence</b>: CC BY-NC 4.0 (NON COMMERCIAL USE ONLY) </p><p><br></p>2025-07-25T14:51:47ZDatasetinfo:eu-repo/semantics/publishedVersiondataset10.6084/m9.figshare.29646311.v1https://figshare.com/articles/dataset/Supplementary_data_tar_gz/29646311CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/296463112025-07-25T14:51:47Z |
| spellingShingle | Supplementary_data.tar.gz héléna vassilieff (19216723) Molecular evolution Caulimoviridae endogenous virus Viral evolution |
| status_str | publishedVersion |
| title | Supplementary_data.tar.gz |
| title_full | Supplementary_data.tar.gz |
| title_fullStr | Supplementary_data.tar.gz |
| title_full_unstemmed | Supplementary_data.tar.gz |
| title_short | Supplementary_data.tar.gz |
| title_sort | Supplementary_data.tar.gz |
| topic | Molecular evolution Caulimoviridae endogenous virus Viral evolution |