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 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.