Next-Generation Sequencing of Crown and Rhizome Transcriptome from an Upland, Tetraploid Switchgrass
2012
Palmer, Nathan A. | Saathoff, Aaron J. | Kim, Jaehyoung | Benson, Andrew | Tobias, Christian M. | Twigg, Paul | Vogel, Kenneth P. | Madhavan, Soundararajan | Sarath, Gautam
The crown and rhizome transcriptome of a winter-adapted, upland tetraploid switchgrass cultivar Summer, was investigated using the Roche 454-FLX pyrosequencing platform. In all approximately 1 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. Blast2Go 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 the Sorghum bicolor genome. Singleton sequences while displaying significant matches to Sorghum bicolor, also contained sequences matching non-plant species. Comparisons of the 454 dataset to exiting EST collections resulted in the identification of 30,177 sequences that appeared to be “novel” to the below-ground transcriptome of switchgrass. Novel 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 potentially cultivar Summer 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 transcripts 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 the post-anthesis, seed maturation stage of plant development.
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