Data from: Generation of transcript assemblies and identification of single nucleotide polymorphisms from seven lowland and upland cultivars of switchgrass

Switchgrass (Panicum virgatum) is a North American perennial prairie
species that has been used as a rangeland and forage crop and has recently
been targeted as a potential biofuel feedstock species. Switchgrass, which
occurs as tetraploid and octoploid forms, is classified into lowland or
upland ecotypes that differ in growth phenotypes and adaptation to
distinct habitats. Using RNA-sequencing reads derived from crown, young
shoot and leaf tissues, we generated sequence data from seven switchgrass
cultivars, three lowland and four upland, to enable comparative analyses
between switchgrass cultivars and to identify single nucleotide
polymorphisms (SNPs) for use in breeding and genetic analysis. We also
generated individual transcript assemblies for each of the cultivars.
Transcript data indicate that subgenomes of octoploid switchgrass are not
substantially different from subgenomes of tetraploids as expected for an
autopolyploid origin of switchgrass octoploids. Using RNA-sequencing reads
aligned to the switchgrass Release 0 AP13 reference genome, we identified
1,305,976 high-confidence SNPs. Of these SNPs, 438,464 were unique to
lowland cultivars, but only 12,002 were found in all lowlands. Conversely,
723,678 SNPs were unique to upland cultivars with only 34,665 observed in
all uplands. Comparison of our high-confidence transcriptome-derived SNPs
with SNPs previously identified in a genotyping-by-sequencing study of an
association panel revealed limited overlap between the two methods,
highlighting the utility of transcriptome-based SNP discovery in
augmenting genome diversity polymorphism datasets. The transcript and SNP
data described here provide a useful resource for switchgrass gene
annotation and marker-based analyses of the switchgrass genome.