Data from: Targeted multiplex next-generation sequencing: Advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics

• Main Authors: Hancock-Hanser, Brittany, Frey, Amy, Leslie, Matthew S., Dutton, Peter H., Archer, Frederick I., Morin, Phillip A., Hancock-Hanser, Brittany L.
• Format: Other/Unknown Material
• Language: unknown
• Published: Zenodo 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
• Online Access: https://doi.org/10.5061/dryad.cv35b

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.txt FASTA file of fin whale nuclear loci for capture array design and sequence read assembly. Beaked_75nucloci_fasta FASTA file of beaked whale nuclear loci for capture array design and sequence read assembly. Cmyd_nucFrags_fasta FASTA file of green turtle nuclear loci for capture array design and ...