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

Authors

Nathan A. Palmer, USDAFollow
Aaron J. Saathoff, USDA
Jaehyoung Kim, University of Nebraska-Lincoln
Andrew Benson, University of Nebraska-LincolnFollow
Christian M. Tobias, USDA-ARS
Paul G. Twigg, University of Nebraska at KearneyFollow
Kenneth P. Vogel, University of Nebraska-LincolnFollow
Soundararajan Madhavan, University of Nebraska-LincolnFollow
Gautam Sarath, United States Department of Agriculture -Agricultural Research ServiceFollow

Date of this Version

2012

Citation

Palmer, Nathan A., Aaron J. Saathoff, Jaehyoung Kim, Andrew Benson, Christian M. Tobias, Paul Twig, Kenneth P. Vogel, Soudnararajan Madhavan, and Gautam Sarath. 2012. Next-Generation sequencing of crown and rhizome transcriptome from and upland, tetrapoloid switchgrass. Bioenergy Research.5:649-661. DOI 10.1007/s12155-011-9171-1

Comments

U.S. government work

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.