Data from: Optimizing exome captures in species with large genomes using species-specific repetitive DNA blocker

Large and highly repetitive genomes are common. However, research
interests usually lie within the non-repetitive parts of the genome, as
they are more likely functional, and can be used to answer questions
related to adaptation, selection, and evolutionary history. Exome capture
is a cost-effective method for providing sequencing data from
protein-coding parts of the genes. C0t-1 DNA blockers consist of
repetitive DNA and are used in exome captures to prevent the hybridization
of repetitive DNA sequences to capture baits or bait-bound genomic DNA.
Universal blockers target repetitive regions shared by many species, while
species-specific c0t-1 DNA is prepared from the DNA of the studied
species, thus perfectly matching the repetitive DNA contents of the
species. So far the use of species-specific c0t-1 DNA has been limited to
a few model species. Here, we evaluated the performance of blocker
treatments in exome captures of Pinus sylvestris, a widely distributed
conifer species with a large (> 20 Gbp) and highly repetitive
genome. We compared treatment with a commercial universal blocker to
treatments with species-specific c0t-1 (30,000 ng and 60,000 ng).
Species-specific c0t-1 captured more unique exons than the initial set of
targets leading to increased SNP discovery and reduced sequencing of
tandem repeats compared to the universal blocker. Based on our results, we
recommend optimizing exome captures by using at least 60,000 ng
species-specific c0t-1 DNA. It is relatively easy and fast to prepare and
can also be used with existing bait set designs.