Data from: Nucleotide polymorphism and copy number variant detection using exome capture and next generation sequencing in the polyploid grass Panicum virgatum

Switchgrass (Panicum virgatum) is a polyploid, outcrossing grass species
native to North America and has recently been recognized as a potential
biofuel feedstock crop. Significant phenotypic variation including ploidy
is present across the two primary ecotypes of switchgrass, referred to as
upland and lowland switchgrass. The tetraploid switchgrass genome is
approximately 1400 Mbp, split between two subgenomes, with significant
repetitive sequence content limiting the efficiency of re-sequencing
approaches for determining genome diversity. To characterize genetic
diversity in upland and lowland switchgrass as a first step in linking
genotype to phenotype, we designed an exome capture probe set based on
transcript assemblies that represent ~50 Mb of annotated switchgrass exome
sequences. We then evaluated and optimized the probe set using solid phase
comparative genome hybridization and liquid phase exome capture followed
by next generation sequencing. Using the optimized probe set, we assessed
variation in the exomes of eight switchgrass genotypes representing
tetraploid lowland and octoploid upland cultivars to benchmark our exome
capture probe set design. We identified ample variation in the switchgrass
genome including 1,395,501 single nucleotide polymorphisms (SNPs), 8,173
putative copy number variants and 3,336 presence/absence variants. While
the majority of the SNPs (84%) detected were biallelic, a substantial
number were tri-allelic with limited occurrence of tetra-allelic
polymorphisms consistent with the heterozygous and polyploid nature of the
switchgrass genome. Collectively, these data demonstrate the efficacy of
exome capture for discovery of genome variation in a polyploid species
with a large, repetitive and heterozygous genome.