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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Online Access: | https://doi.org/10.5061/dryad.1dp6s |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::f8ac2dcf2a6d1a60bb92436c77c41fc0 2023-05-15T13:56:10+02:00 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 en eng Dryad http://dx.doi.org/10.5061/dryad.1dp6s https://dx.doi.org/10.5061/dryad.1dp6s lic_creative-commons 10.5061/dryad.1dp6s oai:easy.dans.knaw.nl:easy-dataset:90000 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:90000 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 re3data_____::r3d100000044 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c metagenomics Genomics/Proteomics Microbial Biology molecular evolution Life sciences medicine and health care geo envir Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2015 fttriple https://doi.org/10.5061/dryad.1dp6s 2023-01-22T16:53:31Z 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 assemblersContigs.zipAlignment of the RpRd domainRdRp_Alignment.faPhylogenetic tree based on RpRd domain alignmentRdRp_Tree.newickValidated SNVsValidated SNVs (CLC Genomic Workbench approach) for all APLV-quasispeciesAPLV_SNVs.xlsxPCA input for dinucleotide bias analysisDinucleotidePCA_131Picornavirales.txt Dataset Antarc* Antarctic Livingston Island Unknown Antarctic Livingston Island ENVELOPE(-60.500,-60.500,-62.600,-62.600) |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
English |
topic |
metagenomics Genomics/Proteomics Microbial Biology molecular evolution Life sciences medicine and health care geo envir |
spellingShingle |
metagenomics Genomics/Proteomics Microbial Biology molecular evolution Life sciences medicine and health care geo envir 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 molecular evolution Life sciences medicine and health care geo envir |
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 assemblersContigs.zipAlignment of the RpRd domainRdRp_Alignment.faPhylogenetic tree based on RpRd domain alignmentRdRp_Tree.newickValidated SNVsValidated SNVs (CLC Genomic Workbench approach) for all APLV-quasispeciesAPLV_SNVs.xlsxPCA input for dinucleotide bias analysisDinucleotidePCA_131Picornavirales.txt |
format |
Dataset |
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 |
Dryad |
publishDate |
2015 |
url |
https://doi.org/10.5061/dryad.1dp6s |
long_lat |
ENVELOPE(-60.500,-60.500,-62.600,-62.600) |
geographic |
Antarctic Livingston Island |
geographic_facet |
Antarctic Livingston Island |
genre |
Antarc* Antarctic Livingston Island |
genre_facet |
Antarc* Antarctic Livingston Island |
op_source |
10.5061/dryad.1dp6s oai:easy.dans.knaw.nl:easy-dataset:90000 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:90000 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 re3data_____::r3d100000044 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
http://dx.doi.org/10.5061/dryad.1dp6s https://dx.doi.org/10.5061/dryad.1dp6s |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.1dp6s |
_version_ |
1766263533080674304 |