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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ftzenodo:oai:zenodo.org:5004958 2024-09-15T18:00:40+00:00 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 2014-02-20 https://doi.org/10.5061/dryad.n8f30 unknown Zenodo https://doi.org/10.1111/1755-0998.12241 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.n8f30 oai:zenodo.org:5004958 info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode Bioinfomatics Calanus helgolandicus Calanus marshallae Crustaceans Calanus finmarchicus Calanus glacialis Copepoda Calanus hyperboreus Phyloinfomatics info:eu-repo/semantics/other 2014 ftzenodo https://doi.org/10.5061/dryad.n8f3010.1111/1755-0998.12241 2024-07-26T00:44:57Z 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.fasta C. 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.fasta C. 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.fasta C. 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.fasta Microsatellites_Genotypes Table of microsatellite genotyping for species identification of Calanus finmarchicus and C. glacialis Msat_Genotypes_SuppInfo.xlsx Other/Unknown Material Calanus finmarchicus Calanus glacialis Calanus hyperboreus Zooplankton Copepods Zenodo |
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op_collection_id |
ftzenodo |
language |
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Bioinfomatics Calanus helgolandicus Calanus marshallae Crustaceans Calanus finmarchicus Calanus glacialis Copepoda Calanus hyperboreus Phyloinfomatics |
spellingShingle |
Bioinfomatics Calanus helgolandicus Calanus marshallae Crustaceans Calanus finmarchicus Calanus glacialis Copepoda Calanus hyperboreus Phyloinfomatics 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 Crustaceans Calanus finmarchicus Calanus glacialis Copepoda Calanus hyperboreus Phyloinfomatics |
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.fasta C. 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.fasta C. 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.fasta C. 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.fasta Microsatellites_Genotypes Table of microsatellite genotyping for species identification of Calanus finmarchicus and C. glacialis Msat_Genotypes_SuppInfo.xlsx |
format |
Other/Unknown Material |
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 |
Zenodo |
publishDate |
2014 |
url |
https://doi.org/10.5061/dryad.n8f30 |
genre |
Calanus finmarchicus Calanus glacialis Calanus hyperboreus Zooplankton Copepods |
genre_facet |
Calanus finmarchicus Calanus glacialis Calanus hyperboreus Zooplankton Copepods |
op_relation |
https://doi.org/10.1111/1755-0998.12241 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.n8f30 oai:zenodo.org:5004958 |
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.n8f3010.1111/1755-0998.12241 |
_version_ |
1810437839139110912 |