U.S. Department of EnergyOffice of Scientific and Technical Information
Data from: Nucleotide polymorphism and copy number variant detection using exome capture and next generation sequencing in the polyploid grass Panicum virgatum
Abstract
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 numbermore »
- Authors:
-
- Michigan State Univ., East Lansing, MI (United States); OSTI
- Michigan State Univ., East Lansing, MI (United States)
- Univ. of Wisconsin, Madison, WI (United States)
- Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States)
- Roche-NimbleGen, Madison, WI (United States)
- Publication Date:
- DOE Contract Number:
- FC02-07ER64494
- Research Org.:
- Great Lakes Bioenergy Research Center, Madison, WI (United States); Univ. of Wisconsin, Madison, WI (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- Subject:
- 09 BIOMASS FUELS
- OSTI Identifier:
- 1874205
- DOI:
- https://doi.org/10.5061/dryad.b52p5
Citation Formats
Evans, Joseph, Kim, Jeongwoon, Childs, Kevin L., Vaillancourt, Brieanne, Crisovan, Emily, Nandety, Aruna, Gerhardt, Daniel J., Richmond, Todd A., Jeddeloh, Jeffrey A., Kaeppler, Shawn M., Casler, Michael D., and Buell, C. Robin. Data from: Nucleotide polymorphism and copy number variant detection using exome capture and next generation sequencing in the polyploid grass Panicum virgatum. United States: N. p., 2015.
Web. doi:10.5061/dryad.b52p5.
Evans, Joseph, Kim, Jeongwoon, Childs, Kevin L., Vaillancourt, Brieanne, Crisovan, Emily, Nandety, Aruna, Gerhardt, Daniel J., Richmond, Todd A., Jeddeloh, Jeffrey A., Kaeppler, Shawn M., Casler, Michael D., & Buell, C. Robin. Data from: Nucleotide polymorphism and copy number variant detection using exome capture and next generation sequencing in the polyploid grass Panicum virgatum. United States. doi:https://doi.org/10.5061/dryad.b52p5
Evans, Joseph, Kim, Jeongwoon, Childs, Kevin L., Vaillancourt, Brieanne, Crisovan, Emily, Nandety, Aruna, Gerhardt, Daniel J., Richmond, Todd A., Jeddeloh, Jeffrey A., Kaeppler, Shawn M., Casler, Michael D., and Buell, C. Robin. 2015.
"Data from: Nucleotide polymorphism and copy number variant detection using exome capture and next generation sequencing in the polyploid grass Panicum virgatum". United States. doi:https://doi.org/10.5061/dryad.b52p5. https://www.osti.gov/servlets/purl/1874205. Pub date:Sat Jun 13 00:00:00 EDT 2015
@article{osti_1874205,
title = {Data from: Nucleotide polymorphism and copy number variant detection using exome capture and next generation sequencing in the polyploid grass Panicum virgatum},
author = {Evans, Joseph and Kim, Jeongwoon and Childs, Kevin L. and Vaillancourt, Brieanne and Crisovan, Emily and Nandety, Aruna and Gerhardt, Daniel J. and Richmond, Todd A. and Jeddeloh, Jeffrey A. and Kaeppler, Shawn M. and Casler, Michael D. and Buell, C. Robin},
abstractNote = {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.},
doi = {10.5061/dryad.b52p5},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Sat Jun 13 00:00:00 EDT 2015},
month = {Sat Jun 13 00:00:00 EDT 2015}
}