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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Bibliographic Details
Main Authors: Hancock-Hanser, Brittany, Frey, Amy, Leslie, Matthew S., Dutton, Peter H., Archer, Frederick I., Morin, Phillip A., Hancock-Hanser, Brittany L.
Format: Dataset
Language:English
Published: Dryad 2012
Subjects:
Balaenoptera physalus
Next-generation sequencing
DNA capture array
Mesoplodon densirostris
Chelonia mydas
Ziphius cavirostris
Physeter macrocephalus
Tursiops truncatus
green sea turtle
cetacean
Fin whale
Sperm whale
Online Access:https://dx.doi.org/10.5061/dryad.cv35b
https://datadryad.org/stash/dataset/doi:10.5061/dryad.cv35b
Description
Summary: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 ... : 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 read assembly.SpermWhale_50nucSeqs_SNPdisco_FastaFASTA file of sperm whale nuclear loci for capture array design and sequence read assembly.Spinner-Spotted_85nuc_loci_FastaFASTA file of bottlenose dolphin nuclear loci for capture array design and sequence read assembly of spinner and spotted dolphins.BeakedWhale_arrayeArray data files for capture array designCmyd_arrayeArray data files for capture array designFinWhale_arrayeArray data files for capture array designSpermWhale_ArrayeArray data files for capture array designSpinner-SpottedDolphin_ArrayeArray data files for capture array designmerged vcf to genotypeR script for converting 'vcf' data from SNP pipeline to a single ...

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