DOI: 10.5061/dryad.8f73k
title: Data from: Generation of transcript assemblies and identification of single nucleotide polymorphisms from seven lowland and upland cultivars of switchgrass

description: 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.
description: all_switchgrass_SNPs_filtered.txtSNPs identified within the switchgrass cultivars Alamo, SG5, Wabasso, Pathfinder, Trailblazer, Carthage and Shelter.all_switchgrass_SNPs_with_context_sequence.txtThis file contains context sequence surrounding SNPs identified within the switchgrass cultivars Alamo, SG5, Wabasso, Pathfinder, Trailblazer, Carthage and Shelter.Alamo_transcript_assemblies_all_isoforms.fastaRNA-seq transcript assemblies created with Velvet/Oases from the switchgrass cultivar Alamo. This file includes all transcript isoforms.Alamo_transcript_assemblies_representative_isoforms.fastaRNA-seq transcript assemblies created with Velvet/Oases from the switchgrass cultivar Alamo. This file includes only representative transcript.Carthage_transcript_assemblies_all_isoforms.fastaRNA-seq transcript assemblies created with Velvet/Oases from the switchgrass cultivar Carthage. This file includes all transcript isoforms.Carthage_transcript_assemblies_representative_isoforms.fastaRNA-seq transcript assemblies created with Velvet/Oases from the switchgrass cultivar Carthage. This file includes only representative transcript.Pathfinder_transcript_assemblies_all_isoforms.fastaRNA-seq transcript assemblies created with Velvet/Oases from the switchgrass cultivar Pathfinder. This file includes all transcript isoforms.Pathfinder_transcript_assemblies_representative_isoforms.fastaRNA-seq transcript assemblies created with Velvet/Oases from the switchgrass cultivar Pathfinder. This file includes only representative transcript.SG5_transcript_assemblies_all_isoforms.fastaRNA-seq transcript assemblies created with Velvet/Oases from the switchgrass cultivar SG5. This file includes all transcript isoforms.SG5_transcript_assemblies_representative_isoforms.fastaRNA-seq transcript assemblies created with Velvet/Oases from the switchgrass cultivar SG5. This file includes only representative transcript.Shelter_transcript_assemblies_all_isoforms.fastaRNA-seq transcript assemblies created with Velvet/Oases from the switchgrass cultivar Shelter. This file includes all transcript isoforms.Shelter_transcript_assemblies_representative_isoforms.fastaRNA-seq transcript assemblies created with Velvet/Oases from the switchgrass cultivar Shelter. This file includes only representative transcript.Trailblazer_transcript_assemblies_all_isoforms.fastaRNA-seq transcript assemblies created with Velvet/Oases from the switchgrass cultivar Trailblazer. This file includes all transcript isoforms.Trailblazer_transcript_assemblies_representative_isoforms.fastaRNA-seq transcript assemblies created with Velvet/Oases from the switchgrass cultivar Trailblazer. This file includes only representative transcript.Wabasso_transcript_assemblies_all_isoforms.fastaRNA-seq transcript assemblies created with Velvet/Oases from the switchgrass cultivar Wabasso. This file includes all transcript isoforms.Wabasso_transcript_assemblies_representative_isoforms.fastaRNA-seq transcript assemblies created with Velvet/Oases from the switchgrass cultivar Wabasso. This file includes only representative transcript.combined_switchgrass_transcript_assemblies_all_isoforms.fastaRNA-seq transcript assemblies created with Velvet/Oases using seven switchgrass cultivars Alamo, SG5, Wabasso, Pathfinder, Shelter, Trailblazer and Carthage. This file includes all transcript isoforms.combined_switchgrass_transcript_assemblies_representative_isoforms.fastaRNA-seq transcript assemblies created with Velvet/Oases using seven switchgrass cultivars Alamo, SG5, Wabasso, Pathfinder, Shelter, Trailblazer and Carthage. This file includes only representative transcript.