BioEnergy Research

, Volume 5, Issue 3, pp 649–661

Next-Generation Sequencing of Crown and Rhizome Transcriptome from an Upland, Tetraploid Switchgrass

  • Nathan A. Palmer
  • Aaron J. Saathoff
  • Jaehyoung Kim
  • Andrew Benson
  • Christian M. Tobias
  • Paul Twigg
  • Kenneth P. Vogel
  • Soundararajan Madhavan
  • Gautam Sarath
Article

DOI: 10.1007/s12155-011-9171-1

Cite this article as:
Palmer, N.A., Saathoff, A.J., Kim, J. et al. Bioenerg. Res. (2012) 5: 649. doi:10.1007/s12155-011-9171-1

Abstract

The crown and rhizome transcriptome of an upland tetraploid switchgrass cultivar cv Summer well adapted to the upper Midwest was investigated using the Roche 454-FLX pyrosequencing platform. Overall, approximately one million reads consisting of 216 million bases were assembled into 27,687 contigs and 43,094 singletons. Analyses of these sequences revealed minor contamination with non-plant sequences (< 0.5%), indicating that a majority were for transcripts coded by the switchgrass genome. Blast2Gos comparisons resulted in the annotation of ~65% of the contig sequences and ~40% of the singleton sequences. Contig sequences were mostly homologous to other plant sequences, dominated by matches to Sorghum bicolor genome. Singleton sequences, while displaying significant matches to S. bicolor, also contained sequences matching non-plant species. Comparisons of the 454 dataset to existing EST collections resulted in the identification of 30,177 new sequences. These new sequences coded for a number of different proteins and a selective analysis of two categories, namely, peroxidases and transcription factors, resulted in the identification of specific peroxidases and a number of low-abundance transcription factors expected to be involved in chromatin remodeling. KEGG maps for glycolysis and sugar metabolism showed high levels of transcript coding for enzymes involved in primary metabolism. The assembly provided significant insights into the status of these tissues and broadly indicated that there was active metabolism taking place in the crown and rhizomes at post-anthesis, the seed maturation stage of plant development.

Keywords

454 FLX pyrosequencingBioenergyCrowns and rhizomesSwitchgrassTranscriptomeTranscription factors

Supplementary material

12155_2011_9171_MOESM1_ESM.docx (15 kb)
Table S1The 50 most abundant contigs in switchgrass crown and rhizome transcriptome assembly (DOCX 14 kb)
12155_2011_9171_MOESM2_ESM.docx (16 kb)
Table S2Comparison of assembly outcomes for selected plant transcriptomes performed by 454 pyrosequencing1 (DOCX 15 kb)

Copyright information

© Springer Science+Business Media, LLC. (outside the USA) 2011

Authors and Affiliations

  • Nathan A. Palmer
    • 1
    • 6
  • Aaron J. Saathoff
    • 1
    • 6
  • Jaehyoung Kim
    • 2
  • Andrew Benson
    • 2
  • Christian M. Tobias
    • 3
  • Paul Twigg
    • 4
  • Kenneth P. Vogel
    • 1
    • 6
  • Soundararajan Madhavan
    • 5
  • Gautam Sarath
    • 1
    • 6
    • 7
  1. 1.Grain, Forage and Bioenergy Research UnitUSDA Central-East Biomass Regional CenterLincolnUSA
  2. 2.Center for Applied Genomics and Ecology, Department of Food Science and TechnologyUniversity of Nebraska at LincolnLincolnUSA
  3. 3.Genomics and Gene Discovery Research Unit, Western Regional Research CenterUSDA-ARSAlbanyUSA
  4. 4.Biology DepartmentUniversity of Nebraska at KearneyKearneyUSA
  5. 5.Department of BiochemistryUniversity of Nebraska at LincolnLincolnUSA
  6. 6.Department of Agronomy and HorticultureUniversity of Nebraska at LincolnLincolnUSA
  7. 7.Grain, Forage and Bioenergy Research UnitUSDA-ARSLincolnUSA