Location: Grain, Forage, and Bioenergy ResearchTitle: Next generation sequencing of crown and rhizome transcriptome from an upland, tetraploid switchgrass) Author
|Palmer, Nathan - Nate|
Submitted to: BioEnergy Research
Publication Type: Peer reviewed journal
Publication Acceptance Date: 11/28/2011
Publication Date: 9/1/2012
Publication URL: http://handle.nal.usda.gov/10113/55922
Citation: Palmer, N.A., Saathoff, A.J., Kim, J., Benson, A., Tobias, C.M., Twigg, P., Vogel, K.P., Madhavan, S., Sarath, G. 2012. Next generation sequencing of crown and rhizome transcriptome from an upland, tetraploid switchgrass. BioEnergy Research. 5:649-661. DOI 10.1007/s12155-011-9171-1. Interpretive Summary: Switchgrass is a key species being evaluated for use as a lignocellulosic bioenergy crop. An essential trait for a perennial bioenergy plant such as switchgrass is the ability to regrow shoots (tillers) every year without having any significant winter kill. Since this regrowth occurs from the below-ground crown and rhizome tissues understanding the molecular processes underpinning this yearly cycle of growth and dormancy are likely to provide insights into cellular factors that impact perenniality and winter hardiness. In this study crown and rhizome tissues obtained from a switchgrass cultivar (cv Summer) that shows good winter hardiness were used as a source to obtain molecular information. Messenger RNA were extracted from these tissues and analyzed on a next-generation DNA sequencer. This instrument provided a very large number of sequences, which were subsequently annotated using tools in bioinformatics. These annotations made it possible to get a snap shot of the biological and metabolic status of the tissue. Overall, our first of a kind data, can now serve as a foundation to explore changes occurring at the molecular level in below-ground tissues obtained from switchgrass plants with divergent responses to cold temperatures. In the long-term these datasets will provide information that can be applied in breeding programs to improve this important bioenergy crop.
Technical Abstract: 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.