Data from: Molecular Inversion Probes for targeted resequencing in non-model organisms

Applications that require resequencing of hundreds or thousands of
predefined genomic regions in numerous samples are common in studies of
non-model organisms. However few approaches at the scale intermediate
between multiplex PCR and sequence capture methods are available. Here we
explored the utility of Molecular Inversion Probes (MIPs) for the
medium-scale targeted resequencing in a non-model system. Markers
targeting 112 bp of exonic sequence were designed from transcriptome of
Lissotriton newts. We assessed performance of 248 MIP markers in a sample
of 85 individuals. Among the 234 (94.4%) successfully amplified markers
80% had median coverage within one order of magnitude, indicating
relatively uniform performance; coverage uniformity across individuals was
also high. In the analysis of polymorphism and segregation within family,
77% of 248 tested MIPs were confirmed as single copy Mendelian markers.
Genotyping concordance assessed using replicate samples exceeded 99%. MIP
markers for targeted resequencing have a number of advantages: high
specificity, high multiplexing level, low sample requirement,
straightforward laboratory protocol, no need for preparation of genomic
libraries and no ascertainment bias. We conclude that MIP markers provide
an effective solution for resequencing targets of tens or hundreds of kb
in any organism and in a large number of samples.