Data from: Double-digest RAD Sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with non-model organisms
Research in evolutionary biology involving nonmodel organisms is rapidly shifting from using traditional molecular markers such as mtDNA and microsatellites to higher throughput SNP genotyping methodologies to address questions in population genetics, phylogenetics and genetic mapping. Restriction s...
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ftdans:oai:easy.dans.knaw.nl:easy-dataset:88494 2023-07-02T03:30:55+02:00 Data from: Double-digest RAD Sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with non-model organisms Recknagel, Hans Jacobs, Arne Herzyk, Pawel Elmer, Kathryn R. 2015-03-19T16:33:27.000+01:00 http://nbn-resolving.org/urn:nbn:nl:ui:13-49-mvs6 https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:88494 unknown doi:10.5061/dryad.7tb72/1 doi:10.5061/dryad.7tb72/2 doi:10.5061/dryad.7tb72/3 doi:10.5061/dryad.7tb72/4 doi:10.5061/dryad.7tb72/5 doi:10.5061/dryad.7tb72/6 doi:10.5061/dryad.7tb72/7 doi:10.5061/dryad.7tb72/8 doi:10.5061/dryad.7tb72/9 doi:10.5061/dryad.7tb72/10 doi:10.5061/dryad.7tb72/11 doi:10.5061/dryad.7tb72/12 doi:10.5061/dryad.7tb72/13 doi:10.5061/dryad.7tb72/14 doi:10.5061/dryad.7tb72/15 doi:10.5061/dryad.7tb72/16 doi:10.5061/dryad.7tb72/17 doi:10.5061/dryad.7tb72/21 doi:10.5061/dryad.7tb72/19 doi:10.5061/dryad.7tb72/20 doi:10.1111/1755-0998.12406 PMID:25808755 http://nbn-resolving.org/urn:nbn:nl:ui:13-49-mvs6 doi:10.5061/dryad.7tb72 https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:88494 OPEN_ACCESS: The data are archived in Easy, they are accessible elsewhere through the DOI https://dans.knaw.nl/en/about/organisation-and-policy/legal-information/DANSLicence.pdf Life sciences medicine and health care 2015 ftdans https://doi.org/10.5061/dryad.7tb72/110.5061/dryad.7tb72/210.5061/dryad.7tb72/310.5061/dryad.7tb72/410.5061/dryad.7tb72/510.5061/dryad.7tb72/610.5061/dryad.7tb72/710.5061/dryad.7tb72/810.5061/dryad.7tb72/910.5061/dryad.7tb72/1010.5061/dryad.7tb72/1110.506 2023-06-13T13:18:35Z Research in evolutionary biology involving nonmodel organisms is rapidly shifting from using traditional molecular markers such as mtDNA and microsatellites to higher throughput SNP genotyping methodologies to address questions in population genetics, phylogenetics and genetic mapping. Restriction site associated DNA sequencing (RAD sequencing or RADseq) has become an established method for SNP genotyping on Illumina sequencing platforms. Here, we developed a protocol and adapters for double-digest RAD sequencing for Ion Torrent (Life Technologies; Ion Proton, Ion PGM) semiconductor sequencing. We sequenced thirteen genomic libraries of three different nonmodel vertebrate species on Ion Proton with PI chips: Arctic charr Salvelinus alpinus, European whitefish Coregonus lavaretus and common lizard Zootoca vivipara. This resulted in ~962 million single-end reads overall and a mean of ~74 million reads per library. We filtered the genomic data using Stacks, a bioinformatic tool to process RAD sequencing data. On average, we obtained ~11 000 polymorphic loci per library of 6–30 individuals. We validate our new method by technical and biological replication, by reconstructing phylogenetic relationships, and using a hybrid genetic cross to track genomic variants. Finally, we discuss the differences between using the different sequencing platforms in the context of RAD sequencing, assessing possible advantages and disadvantages. We show that our protocol can be used for Ion semiconductor sequencing platforms for the rapid and cost-effective generation of variable and reproducible genetic markers. Other/Unknown Material Arctic charr Arctic Salvelinus alpinus Data Archiving and Networked Services (DANS): EASY (KNAW - Koninklijke Nederlandse Akademie van Wetenschappen) Arctic |
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Data Archiving and Networked Services (DANS): EASY (KNAW - Koninklijke Nederlandse Akademie van Wetenschappen) |
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Life sciences medicine and health care |
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Life sciences medicine and health care Recknagel, Hans Jacobs, Arne Herzyk, Pawel Elmer, Kathryn R. Data from: Double-digest RAD Sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with non-model organisms |
topic_facet |
Life sciences medicine and health care |
description |
Research in evolutionary biology involving nonmodel organisms is rapidly shifting from using traditional molecular markers such as mtDNA and microsatellites to higher throughput SNP genotyping methodologies to address questions in population genetics, phylogenetics and genetic mapping. Restriction site associated DNA sequencing (RAD sequencing or RADseq) has become an established method for SNP genotyping on Illumina sequencing platforms. Here, we developed a protocol and adapters for double-digest RAD sequencing for Ion Torrent (Life Technologies; Ion Proton, Ion PGM) semiconductor sequencing. We sequenced thirteen genomic libraries of three different nonmodel vertebrate species on Ion Proton with PI chips: Arctic charr Salvelinus alpinus, European whitefish Coregonus lavaretus and common lizard Zootoca vivipara. This resulted in ~962 million single-end reads overall and a mean of ~74 million reads per library. We filtered the genomic data using Stacks, a bioinformatic tool to process RAD sequencing data. On average, we obtained ~11 000 polymorphic loci per library of 6–30 individuals. We validate our new method by technical and biological replication, by reconstructing phylogenetic relationships, and using a hybrid genetic cross to track genomic variants. Finally, we discuss the differences between using the different sequencing platforms in the context of RAD sequencing, assessing possible advantages and disadvantages. We show that our protocol can be used for Ion semiconductor sequencing platforms for the rapid and cost-effective generation of variable and reproducible genetic markers. |
author |
Recknagel, Hans Jacobs, Arne Herzyk, Pawel Elmer, Kathryn R. |
author_facet |
Recknagel, Hans Jacobs, Arne Herzyk, Pawel Elmer, Kathryn R. |
author_sort |
Recknagel, Hans |
title |
Data from: Double-digest RAD Sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with non-model organisms |
title_short |
Data from: Double-digest RAD Sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with non-model organisms |
title_full |
Data from: Double-digest RAD Sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with non-model organisms |
title_fullStr |
Data from: Double-digest RAD Sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with non-model organisms |
title_full_unstemmed |
Data from: Double-digest RAD Sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with non-model organisms |
title_sort |
data from: double-digest rad sequencing using ion proton semiconductor platform (ddradseq-ion) with non-model organisms |
publishDate |
2015 |
url |
http://nbn-resolving.org/urn:nbn:nl:ui:13-49-mvs6 https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:88494 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic charr Arctic Salvelinus alpinus |
genre_facet |
Arctic charr Arctic Salvelinus alpinus |
op_relation |
doi:10.5061/dryad.7tb72/1 doi:10.5061/dryad.7tb72/2 doi:10.5061/dryad.7tb72/3 doi:10.5061/dryad.7tb72/4 doi:10.5061/dryad.7tb72/5 doi:10.5061/dryad.7tb72/6 doi:10.5061/dryad.7tb72/7 doi:10.5061/dryad.7tb72/8 doi:10.5061/dryad.7tb72/9 doi:10.5061/dryad.7tb72/10 doi:10.5061/dryad.7tb72/11 doi:10.5061/dryad.7tb72/12 doi:10.5061/dryad.7tb72/13 doi:10.5061/dryad.7tb72/14 doi:10.5061/dryad.7tb72/15 doi:10.5061/dryad.7tb72/16 doi:10.5061/dryad.7tb72/17 doi:10.5061/dryad.7tb72/21 doi:10.5061/dryad.7tb72/19 doi:10.5061/dryad.7tb72/20 doi:10.1111/1755-0998.12406 PMID:25808755 http://nbn-resolving.org/urn:nbn:nl:ui:13-49-mvs6 doi:10.5061/dryad.7tb72 https://easy.dans.knaw.nl/ui/datasets/id/easy-dataset:88494 |
op_rights |
OPEN_ACCESS: The data are archived in Easy, they are accessible elsewhere through the DOI https://dans.knaw.nl/en/about/organisation-and-policy/legal-information/DANSLicence.pdf |
op_doi |
https://doi.org/10.5061/dryad.7tb72/110.5061/dryad.7tb72/210.5061/dryad.7tb72/310.5061/dryad.7tb72/410.5061/dryad.7tb72/510.5061/dryad.7tb72/610.5061/dryad.7tb72/710.5061/dryad.7tb72/810.5061/dryad.7tb72/910.5061/dryad.7tb72/1010.5061/dryad.7tb72/1110.506 |
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