Next-Generation Sequencing of Crown and Rhizome Transcriptome from an Upland, Tetraploid Switchgrass
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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
Published online: 13 December 2011 # Springer Science+Business Media, LLC. (outside the USA) 2011
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.
Electronic supplementary material The online version of this article (doi:10.1007/s12155-011-9171-1) contains supplementary material, which is available to authorized users. N. A. Palmer : A. J. Saathoff : K. P. Vogel : G. Sarath Grain, Forage and Bioenergy Research Unit, USDA Central-East Biomass Regional Center, Lincoln, NE 68583-0937, USA J. Kim : A. Benson Center for Applied Genomics and Ecology, Department of Food Science and Technology, University of Nebraska at Lincoln, Lincoln, NE 68583, USA C. M. Tobias Genomics and Gene Discovery Research Unit, Western Regional Research Center, USDA-ARS, Albany, CA 94710, USA P. Twigg Biology Department, University of Nebraska at Kearney, Kearney, NE 68849, USA
S. Madhavan Department of Biochemistry, University of Nebraska at Lincoln, Lincoln, NE 68588-0664, USA N. A. Palmer : A. J. Saathoff : K. P. Vogel : G. Sarath Department of Agronomy and Horticulture, University of Nebraska at Lincoln, Lincoln, NE 68583, USA
G. Sarath (*) Grain, Forage and Bioenergy Research Unit, USDA-ARS, 137 Keim Hall
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