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

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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.

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Acknowledgements

We thank Steve Masterson and Patrick Callahan for excellent technical support. This work was supported by the Office of Science (BER), US Department of Energy Grant Number DE-AI02-09ER64829, and USDA-ARS CRIS project 5440-21000-028-00D. The US Department of Agriculture, Agricultural Research Service, is an equal opportunity/affirmative action employer and all agency services are available without discrimination. Mention of commercial products and organizations in this manuscript is solely to provide specific information. It does not constitute endorsement by USDA-ARS over other products and organizations not mentioned.

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Authors and Affiliations

  1. Grain, Forage and Bioenergy Research Unit, USDA Central-East Biomass Regional Center, Lincoln, NE, 68583-0937, USA

    Nathan A. Palmer, Aaron J. Saathoff, Kenneth P. Vogel & Gautam Sarath

  2. Center for Applied Genomics and Ecology, Department of Food Science and Technology, University of Nebraska at Lincoln, Lincoln, NE, 68583, USA

    Jaehyoung Kim & Andrew Benson

  3. Genomics and Gene Discovery Research Unit, Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA

    Christian M. Tobias

  4. Biology Department, University of Nebraska at Kearney, Kearney, NE, 68849, USA

    Paul Twigg

  5. Department of Biochemistry, University of Nebraska at Lincoln, Lincoln, NE, 68588-0664, USA

    Soundararajan Madhavan

  6. Department of Agronomy and Horticulture, University of Nebraska at Lincoln, Lincoln, NE, 68583, USA

    Nathan A. Palmer, Aaron J. Saathoff, Kenneth P. Vogel & Gautam Sarath

  7. Grain, Forage and Bioenergy Research Unit, USDA-ARS, 137 Keim Hall, Lincoln, NE, 68583-0937, USA

    Gautam Sarath

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  1. Nathan A. Palmer
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Correspondence to Gautam Sarath.

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Table S1

The 50 most abundant contigs in switchgrass crown and rhizome transcriptome assembly (DOCX 14 kb)

Table S2

Comparison of assembly outcomes for selected plant transcriptomes performed by 454 pyrosequencing1 (DOCX 15 kb)

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Palmer, N.A., Saathoff, A.J., Kim, J. et al. Next-Generation Sequencing of Crown and Rhizome Transcriptome from an Upland, Tetraploid Switchgrass. Bioenerg. Res. 5, 649–661 (2012). https://doi.org/10.1007/s12155-011-9171-1

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