DOI: 10.5061/dryad.cv35b
title: Data from: Targeted multiplex next-generation sequencing: Advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics

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.
description: 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 datafile of genotype and read counts for SNP discovery and genotyping.ngs-mtdna-pipeline-v3.2Mitogenome assembly pipeline R scriptngs-snp-pipeline-v3.2nuclear locus assembly and SNP discovery pipeline R scripts.ngs.funcsR data file used by ngs SNP and mtDNA pipeline scripts.