Data from: Targeted multiplex next-generation sequencing: Advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics
Next-generation sequencing (NGS) is emerging as an efficient and cost-effective tool in population genomic analyses of nonmodel organisms, allowing simultaneous resequencing of many regions of multi-genomic DNA from multiplexed samples. Here, we detail our synthesis of protocols for targeted reseque...
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Data Archiving and Networked Services (DANS)
2020
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Online Access: | https://doi.org/10.5061/dryad.cv35b https://doi.org/10.5061/rd8vd6wcd |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::838191d76ba76c74c883a36ebf209db1 2023-05-15T15:36:43+02:00 Data from: Targeted multiplex next-generation sequencing: Advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics Hancock-Hanser, Brittany Frey, Amy Leslie, Matthew S. Dutton, Peter H. Archer, Frederick I. Morin, Phillip A. Hancock-Hanser, Brittany L. 2020-07-17 https://doi.org/10.5061/dryad.cv35b https://doi.org/10.5061/rd8vd6wcd undefined unknown Data Archiving and Networked Services (DANS) http://dx.doi.org/10.5061/dryad.cv35b https://dx.doi.org/10.5061/dryad.cv35b http://dx.doi.org/10.5061/rd8vd6wcd https://dx.doi.org/10.5061/rd8vd6wcd lic_creative-commons oai:easy.dans.knaw.nl:easy-dataset:82673 10.5061/dryad.cv35b 10.5061/rd8vd6wcd oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:82673 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f re3data_____::r3d100000044 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c Life sciences medicine and health care Balaenoptera physalus Next-generation sequencing DNA capture array Mesoplodon densirostris Chelonia mydas Ziphius cavirostris Physeter macrocephalus Tursiops truncatus conservation green sea turtle cetacean population structure info envir Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2020 fttriple https://doi.org/10.5061/dryad.cv35b https://doi.org/10.5061/rd8vd6wcd 2023-01-22T17:13:48Z Next-generation sequencing (NGS) is emerging as an efficient and cost-effective tool in population genomic analyses of nonmodel organisms, allowing simultaneous resequencing of many regions of multi-genomic DNA from multiplexed samples. Here, we detail our synthesis of protocols for targeted resequencing of mitochondrial and nuclear loci by generating indexed genomic libraries for multiplexing up to 100 individuals in a single sequencing pool, and then enriching the pooled library using custom DNA capture arrays. Our use of DNA sequence from one species to capture and enrich the sequencing libraries of another species (i.e. cross-species DNA capture) indicates that efficient enrichment occurs when sequences are up to about 12% divergent, allowing us to take advantage of genomic information in one species to sequence orthologous regions in related species. In addition to a complete mitochondrial genome on each array, we have included between 43 and 118 nuclear loci for low-coverage sequencing of between 18 kb and 87 kb of DNA sequence per individual for single nucleotide polymorphisms discovery from 50 to 100 individuals in a single sequencing lane. Using this method, we have generated a total of over 500 whole mitochondrial genomes from seven cetacean species and green sea turtles. The greater variation detected in mitogenomes relative to short mtDNA sequences is helping to resolve genetic structure ranging from geographic to species-level differences. These NGS and analysis techniques have allowed for simultaneous population genomic studies of mtDNA and nDNA with greater genomic coverage and phylogeographic resolution than has previously been possible in marine mammals and turtles. FinWhale 43loci_Array1_fasta.txtFASTA file of fin whale nuclear loci for capture array design and sequence read assembly.Beaked_75nucloci_fastaFASTA file of beaked whale nuclear loci for capture array design and sequence read assembly.Cmyd_nucFrags_fastaFASTA file of green turtle nuclear loci for capture array design and sequence ... Dataset Balaenoptera physalus Fin whale Physeter macrocephalus Unknown |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Life sciences medicine and health care Balaenoptera physalus Next-generation sequencing DNA capture array Mesoplodon densirostris Chelonia mydas Ziphius cavirostris Physeter macrocephalus Tursiops truncatus conservation green sea turtle cetacean population structure info envir |
spellingShingle |
Life sciences medicine and health care Balaenoptera physalus Next-generation sequencing DNA capture array Mesoplodon densirostris Chelonia mydas Ziphius cavirostris Physeter macrocephalus Tursiops truncatus conservation green sea turtle cetacean population structure info envir Hancock-Hanser, Brittany Frey, Amy Leslie, Matthew S. Dutton, Peter H. Archer, Frederick I. Morin, Phillip A. Hancock-Hanser, Brittany L. Data from: Targeted multiplex next-generation sequencing: Advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics |
topic_facet |
Life sciences medicine and health care Balaenoptera physalus Next-generation sequencing DNA capture array Mesoplodon densirostris Chelonia mydas Ziphius cavirostris Physeter macrocephalus Tursiops truncatus conservation green sea turtle cetacean population structure info envir |
description |
Next-generation sequencing (NGS) is emerging as an efficient and cost-effective tool in population genomic analyses of nonmodel organisms, allowing simultaneous resequencing of many regions of multi-genomic DNA from multiplexed samples. Here, we detail our synthesis of protocols for targeted resequencing of mitochondrial and nuclear loci by generating indexed genomic libraries for multiplexing up to 100 individuals in a single sequencing pool, and then enriching the pooled library using custom DNA capture arrays. Our use of DNA sequence from one species to capture and enrich the sequencing libraries of another species (i.e. cross-species DNA capture) indicates that efficient enrichment occurs when sequences are up to about 12% divergent, allowing us to take advantage of genomic information in one species to sequence orthologous regions in related species. In addition to a complete mitochondrial genome on each array, we have included between 43 and 118 nuclear loci for low-coverage sequencing of between 18 kb and 87 kb of DNA sequence per individual for single nucleotide polymorphisms discovery from 50 to 100 individuals in a single sequencing lane. Using this method, we have generated a total of over 500 whole mitochondrial genomes from seven cetacean species and green sea turtles. The greater variation detected in mitogenomes relative to short mtDNA sequences is helping to resolve genetic structure ranging from geographic to species-level differences. These NGS and analysis techniques have allowed for simultaneous population genomic studies of mtDNA and nDNA with greater genomic coverage and phylogeographic resolution than has previously been possible in marine mammals and turtles. FinWhale 43loci_Array1_fasta.txtFASTA file of fin whale nuclear loci for capture array design and sequence read assembly.Beaked_75nucloci_fastaFASTA file of beaked whale nuclear loci for capture array design and sequence read assembly.Cmyd_nucFrags_fastaFASTA file of green turtle nuclear loci for capture array design and sequence ... |
format |
Dataset |
author |
Hancock-Hanser, Brittany Frey, Amy Leslie, Matthew S. Dutton, Peter H. Archer, Frederick I. Morin, Phillip A. Hancock-Hanser, Brittany L. |
author_facet |
Hancock-Hanser, Brittany Frey, Amy Leslie, Matthew S. Dutton, Peter H. Archer, Frederick I. Morin, Phillip A. Hancock-Hanser, Brittany L. |
author_sort |
Hancock-Hanser, Brittany |
title |
Data from: Targeted multiplex next-generation sequencing: Advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics |
title_short |
Data from: Targeted multiplex next-generation sequencing: Advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics |
title_full |
Data from: Targeted multiplex next-generation sequencing: Advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics |
title_fullStr |
Data from: Targeted multiplex next-generation sequencing: Advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics |
title_full_unstemmed |
Data from: Targeted multiplex next-generation sequencing: Advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics |
title_sort |
data from: targeted multiplex next-generation sequencing: advances in techniques of mitochondrial and nuclear dna sequencing for population genomics |
publisher |
Data Archiving and Networked Services (DANS) |
publishDate |
2020 |
url |
https://doi.org/10.5061/dryad.cv35b https://doi.org/10.5061/rd8vd6wcd |
genre |
Balaenoptera physalus Fin whale Physeter macrocephalus |
genre_facet |
Balaenoptera physalus Fin whale Physeter macrocephalus |
op_source |
oai:easy.dans.knaw.nl:easy-dataset:82673 10.5061/dryad.cv35b 10.5061/rd8vd6wcd oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:82673 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f re3data_____::r3d100000044 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
http://dx.doi.org/10.5061/dryad.cv35b https://dx.doi.org/10.5061/dryad.cv35b http://dx.doi.org/10.5061/rd8vd6wcd https://dx.doi.org/10.5061/rd8vd6wcd |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.cv35b https://doi.org/10.5061/rd8vd6wcd |
_version_ |
1766367084056412160 |