Data from: Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification
Copepods of the genus Calanus are key zooplankton species in temperate to arctic marine ecosystems. Despite their ecological importance, species identification remains challenging. Furthermore, the recent report of hybrids among Calanus species highlights the need for diagnostic nuclear markers in o...
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Online Access: | https://doi.org/10.5061/dryad.n8f30 |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::b2fedd3792c32d7262c833b0ff803d83 2023-05-15T14:59:59+02:00 Data from: Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification Smolina, Irina Kollias, Spyros Poortvliet, Marloes Nielsen, Torkel Lindeque, Penelope Castellani, Claudia Møller, Eva Blanco-Bercial, Leocadio Hoarau, Galice 2014-01-01 https://doi.org/10.5061/dryad.n8f30 undefined unknown Dryad Digital Repository https://dx.doi.org/10.5061/dryad.n8f30 http://dx.doi.org/10.5061/dryad.n8f30 lic_creative-commons 10.5061/dryad.n8f30 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:85235 oai:easy.dans.knaw.nl:easy-dataset:85235 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 re3data_____::r3d100000044 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c Bioinfomatics Calanus helgolandicus Calanus marshallae hybridization Crustaceans systematics Calanus finmarchicus climate change Calanus glacialis Transcriptomics Copepoda Calanus hyperboreus Genome Phyloinfomatics North Atlantic Arctic Ocean Life sciences medicine and health care envir geo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2014 fttriple https://doi.org/10.5061/dryad.n8f30 2023-01-22T16:52:13Z Copepods of the genus Calanus are key zooplankton species in temperate to arctic marine ecosystems. Despite their ecological importance, species identification remains challenging. Furthermore, the recent report of hybrids among Calanus species highlights the need for diagnostic nuclear markers in order to efficiently identify parental species and hybrids. Using Next Generation Sequencing analysis of both the genome and transcriptome from two sibling species, C. finmarchichus and C. glacialis, we developed a panel of 12 nuclear insertion/deletion markers. All the markers showed species specific amplicon length. Furthermore most of the markers were successfully amplified in other Calanus species allowing the molecular identification of C. helgolandicus, C hyperboreus and C. marshallae. C. finmarchicus genome (contigs)Contigs of C. finmarchicus genome assembled with Geneious 6.1.6. Sequencing technology: Ion Torrent, 200 bp. File contain consensus sequences in fastq file.Cfin_Genome_Contigs.fastaC. glacialis genome (contigs)Contigs of C. glacialis genome assembled with Geneious 6.1.6. Sequencing technology: Ion Torrent, 200 bp. File contain consensus sequences in fastq file.Cgla_Genome_Contigs.fastaC. finmarchicus transcriptome (contigs)Contigs of C. finmarchicus transcriptome assembled with Geneious 6.1.6. Sequencing technology: Ion Torrent, 200 bp. File contain consensus sequences in fastq file.Cfin_Transcriptome_Contigs.fastaC. glacialis transcriptome (contigs)Contigs of C. glacialis transcriptome assembled with Geneious 6.1.6. Sequencing technology: Ion Torrent, 200 bp. File contain consensus sequences in fastq file.Cgla_Transcriptome_Contigs.fastaMicrosatellites_GenotypesTable of microsatellite genotyping for species identification of Calanus finmarchicus and C. glacialisMsat_Genotypes_SuppInfo.xlsx Dataset Arctic Arctic Ocean Atlantic Arctic Atlantic-Arctic Calanus finmarchicus Calanus glacialis Calanus hyperboreus Climate change North Atlantic Zooplankton Copepods Unknown Arctic Arctic Ocean |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Bioinfomatics Calanus helgolandicus Calanus marshallae hybridization Crustaceans systematics Calanus finmarchicus climate change Calanus glacialis Transcriptomics Copepoda Calanus hyperboreus Genome Phyloinfomatics North Atlantic Arctic Ocean Life sciences medicine and health care envir geo |
spellingShingle |
Bioinfomatics Calanus helgolandicus Calanus marshallae hybridization Crustaceans systematics Calanus finmarchicus climate change Calanus glacialis Transcriptomics Copepoda Calanus hyperboreus Genome Phyloinfomatics North Atlantic Arctic Ocean Life sciences medicine and health care envir geo Smolina, Irina Kollias, Spyros Poortvliet, Marloes Nielsen, Torkel Lindeque, Penelope Castellani, Claudia Møller, Eva Blanco-Bercial, Leocadio Hoarau, Galice Data from: Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification |
topic_facet |
Bioinfomatics Calanus helgolandicus Calanus marshallae hybridization Crustaceans systematics Calanus finmarchicus climate change Calanus glacialis Transcriptomics Copepoda Calanus hyperboreus Genome Phyloinfomatics North Atlantic Arctic Ocean Life sciences medicine and health care envir geo |
description |
Copepods of the genus Calanus are key zooplankton species in temperate to arctic marine ecosystems. Despite their ecological importance, species identification remains challenging. Furthermore, the recent report of hybrids among Calanus species highlights the need for diagnostic nuclear markers in order to efficiently identify parental species and hybrids. Using Next Generation Sequencing analysis of both the genome and transcriptome from two sibling species, C. finmarchichus and C. glacialis, we developed a panel of 12 nuclear insertion/deletion markers. All the markers showed species specific amplicon length. Furthermore most of the markers were successfully amplified in other Calanus species allowing the molecular identification of C. helgolandicus, C hyperboreus and C. marshallae. C. finmarchicus genome (contigs)Contigs of C. finmarchicus genome assembled with Geneious 6.1.6. Sequencing technology: Ion Torrent, 200 bp. File contain consensus sequences in fastq file.Cfin_Genome_Contigs.fastaC. glacialis genome (contigs)Contigs of C. glacialis genome assembled with Geneious 6.1.6. Sequencing technology: Ion Torrent, 200 bp. File contain consensus sequences in fastq file.Cgla_Genome_Contigs.fastaC. finmarchicus transcriptome (contigs)Contigs of C. finmarchicus transcriptome assembled with Geneious 6.1.6. Sequencing technology: Ion Torrent, 200 bp. File contain consensus sequences in fastq file.Cfin_Transcriptome_Contigs.fastaC. glacialis transcriptome (contigs)Contigs of C. glacialis transcriptome assembled with Geneious 6.1.6. Sequencing technology: Ion Torrent, 200 bp. File contain consensus sequences in fastq file.Cgla_Transcriptome_Contigs.fastaMicrosatellites_GenotypesTable of microsatellite genotyping for species identification of Calanus finmarchicus and C. glacialisMsat_Genotypes_SuppInfo.xlsx |
format |
Dataset |
author |
Smolina, Irina Kollias, Spyros Poortvliet, Marloes Nielsen, Torkel Lindeque, Penelope Castellani, Claudia Møller, Eva Blanco-Bercial, Leocadio Hoarau, Galice |
author_facet |
Smolina, Irina Kollias, Spyros Poortvliet, Marloes Nielsen, Torkel Lindeque, Penelope Castellani, Claudia Møller, Eva Blanco-Bercial, Leocadio Hoarau, Galice |
author_sort |
Smolina, Irina |
title |
Data from: Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification |
title_short |
Data from: Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification |
title_full |
Data from: Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification |
title_fullStr |
Data from: Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification |
title_full_unstemmed |
Data from: Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification |
title_sort |
data from: genome- and transcriptome-assisted development of nuclear insertion/deletion markers for calanus species (copepoda: calanoida) identification |
publisher |
Dryad Digital Repository |
publishDate |
2014 |
url |
https://doi.org/10.5061/dryad.n8f30 |
geographic |
Arctic Arctic Ocean |
geographic_facet |
Arctic Arctic Ocean |
genre |
Arctic Arctic Ocean Atlantic Arctic Atlantic-Arctic Calanus finmarchicus Calanus glacialis Calanus hyperboreus Climate change North Atlantic Zooplankton Copepods |
genre_facet |
Arctic Arctic Ocean Atlantic Arctic Atlantic-Arctic Calanus finmarchicus Calanus glacialis Calanus hyperboreus Climate change North Atlantic Zooplankton Copepods |
op_source |
10.5061/dryad.n8f30 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:85235 oai:easy.dans.knaw.nl:easy-dataset:85235 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 re3data_____::r3d100000044 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
https://dx.doi.org/10.5061/dryad.n8f30 http://dx.doi.org/10.5061/dryad.n8f30 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.n8f30 |
_version_ |
1766332095844581376 |