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.柳枝稷（Switchgrass，Panicum virgatum）是一种多倍体异交草本植物，原产于北美洲，近年来被认定为极具潜力的生物燃料原料作物。在柳枝稷的两个主要生态型（分别称为旱地型和湿地型柳枝稷）中，存在包括倍性在内的显著表型变异。四倍体柳枝稷的基因组大小约为1400 Mbp，分为两个亚基因组；其基因组中存在大量重复序列，限制了重测序方法在解析基因组多样性时的效率。为表征旱地型与湿地型柳枝稷的遗传多样性，作为连接基因型与表型的第一步研究，我们基于转录组组装结果设计了外显子组捕获探针组（exome capture probe set），该组装覆盖了约50 Mb已注释的柳枝稷外显子组序列。随后，我们利用固相比较基因组杂交（solid phase comparative genome hybridization）技术与液相外显子组捕获（liquid phase exome capture）技术，并结合下一代测序（next generation sequencing）技术，对该探针组进行了评估与优化。利用优化后的探针组，我们对8份柳枝稷基因型的外显子组变异进行了分析，这些基因型涵盖了四倍体湿地型与八倍体旱地型栽培品种，以此对我们的外显子组捕获探针组设计进行基准测试。我们在柳枝稷基因组中检测到了丰富的变异，包括1,395,501个单核苷酸多态性（single nucleotide polymorphisms，SNPs）、8,173个潜在拷贝数变异（copy number variants）以及3,336个存在/缺失变异（presence/absence variants）。尽管检测到的大部分SNPs（84%）为双等位型变异，但仍有相当数量为三等位型变异，仅少量出现四等位基因多态性，这与柳枝稷基因组的杂合性与多倍体特性相符。综上，这些数据证明了外显子组捕获技术在具有大型、重复且杂合基因组的多倍体物种中挖掘基因组变异的有效性。