Data from: Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake
RNA viruses exist as complex mixtures of genotypes, known as quasispecies, where the evolution potential resides in the whole community of related genotypes. Quasispecies structure and dynamics have been studied in detail for virus infecting animals and plants but remain unexplored for those infecti...
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ftzenodo:oai:zenodo.org:4943506 2024-09-15T17:44:27+00:00 Data from: Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake López-Bueno, Alberto Rastrojo, Alberto Peiró, Ramon Arenas, Miguel Alcamí, Antonio 2015-07-14 https://doi.org/10.5061/dryad.1dp6s unknown Zenodo https://doi.org/10.1111/mec.13321 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.1dp6s oai:zenodo.org:4943506 info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode metagenomics Genomics/Proteomics Microbial Biology info:eu-repo/semantics/other 2015 ftzenodo https://doi.org/10.5061/dryad.1dp6s10.1111/mec.13321 2024-07-25T18:36:14Z RNA viruses exist as complex mixtures of genotypes, known as quasispecies, where the evolution potential resides in the whole community of related genotypes. Quasispecies structure and dynamics have been studied in detail for virus infecting animals and plants but remain unexplored for those infecting micro-organisms in environmental samples. We report the first metagenomic study of RNA viruses in an Antarctic lake (Lake Limnopolar, Livingston Island). Similar to low-latitude aquatic environments, this lake harbours an RNA virome dominated by positive single-strand RNA viruses from the order Picornavirales probably infecting micro-organisms. Antarctic picorna-like virus 1 (APLV1), one of the most abundant viruses in the lake, does not incorporate any mutation in the consensus sequence from 2006 to 2010 and shows stable quasispecies with low-complexity indexes. By contrast, APLV2-APLV3 are detected in the lake water exclusively in summer samples and are major constituents of surrounding cyanobacterial mats. Their quasispecies exhibit low complexity in cyanobacterial mat, but their run-off-mediated transfer to the lake results in a remarkable increase of complexity that may reflect the convergence of different viral quasispecies from the catchment area or replication in a more diverse host community. This is the first example of viral quasispecies from natural aquatic ecosystems and points to ecological connectivity as a modulating factor of quasispecies complexity. Contigs obtained with Newbler and CLC Genomic Workbench de novo assemblers Contigs.zip Alignment of the RpRd domain RdRp_Alignment.fa Phylogenetic tree based on RpRd domain alignment RdRp_Tree.newick Validated SNVs Validated SNVs (CLC Genomic Workbench approach) for all APLV-quasispecies APLV_SNVs.xlsx PCA input for dinucleotide bias analysis DinucleotidePCA_131Picornavirales.txt Other/Unknown Material Antarc* Antarctic Livingston Island Zenodo |
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metagenomics Genomics/Proteomics Microbial Biology |
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metagenomics Genomics/Proteomics Microbial Biology López-Bueno, Alberto Rastrojo, Alberto Peiró, Ramon Arenas, Miguel Alcamí, Antonio Data from: Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake |
topic_facet |
metagenomics Genomics/Proteomics Microbial Biology |
description |
RNA viruses exist as complex mixtures of genotypes, known as quasispecies, where the evolution potential resides in the whole community of related genotypes. Quasispecies structure and dynamics have been studied in detail for virus infecting animals and plants but remain unexplored for those infecting micro-organisms in environmental samples. We report the first metagenomic study of RNA viruses in an Antarctic lake (Lake Limnopolar, Livingston Island). Similar to low-latitude aquatic environments, this lake harbours an RNA virome dominated by positive single-strand RNA viruses from the order Picornavirales probably infecting micro-organisms. Antarctic picorna-like virus 1 (APLV1), one of the most abundant viruses in the lake, does not incorporate any mutation in the consensus sequence from 2006 to 2010 and shows stable quasispecies with low-complexity indexes. By contrast, APLV2-APLV3 are detected in the lake water exclusively in summer samples and are major constituents of surrounding cyanobacterial mats. Their quasispecies exhibit low complexity in cyanobacterial mat, but their run-off-mediated transfer to the lake results in a remarkable increase of complexity that may reflect the convergence of different viral quasispecies from the catchment area or replication in a more diverse host community. This is the first example of viral quasispecies from natural aquatic ecosystems and points to ecological connectivity as a modulating factor of quasispecies complexity. Contigs obtained with Newbler and CLC Genomic Workbench de novo assemblers Contigs.zip Alignment of the RpRd domain RdRp_Alignment.fa Phylogenetic tree based on RpRd domain alignment RdRp_Tree.newick Validated SNVs Validated SNVs (CLC Genomic Workbench approach) for all APLV-quasispecies APLV_SNVs.xlsx PCA input for dinucleotide bias analysis DinucleotidePCA_131Picornavirales.txt |
format |
Other/Unknown Material |
author |
López-Bueno, Alberto Rastrojo, Alberto Peiró, Ramon Arenas, Miguel Alcamí, Antonio |
author_facet |
López-Bueno, Alberto Rastrojo, Alberto Peiró, Ramon Arenas, Miguel Alcamí, Antonio |
author_sort |
López-Bueno, Alberto |
title |
Data from: Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake |
title_short |
Data from: Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake |
title_full |
Data from: Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake |
title_fullStr |
Data from: Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake |
title_full_unstemmed |
Data from: Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake |
title_sort |
data from: ecological connectivity shapes quasispecies structure of rna viruses in an antarctic lake |
publisher |
Zenodo |
publishDate |
2015 |
url |
https://doi.org/10.5061/dryad.1dp6s |
genre |
Antarc* Antarctic Livingston Island |
genre_facet |
Antarc* Antarctic Livingston Island |
op_relation |
https://doi.org/10.1111/mec.13321 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.1dp6s oai:zenodo.org:4943506 |
op_rights |
info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.1dp6s10.1111/mec.13321 |
_version_ |
1810492054736732160 |