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Open Access Research article

A detailed gene expression study of the Miscanthus genus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes

Adam Barling12, Kankshita Swaminathan1, Therese Mitros34, Brandon T James12, Juliette Morris1, Ornella Ngamboma1, Megan C Hall37, Jessica Kirkpatrick12, Magdy Alabady18, Ashley K Spence59, Matthew E Hudson12, Daniel S Rokhsar346 and Stephen P Moose12*

Author Affiliations

1 Energy Biosciences Institute, Institute for Genomic Biology, University of Illinois Urbana, 1206 West Gregory Drive, Urbana, IL 61801, USA

2 Crop Sciences, University of Illinois, AW-101 Turner Hall, 1102 S. Goodwin Avenue, Urbana, IL 61801, USA

3 Energy Biosciences Institute, University of California, 135 Energy Biosciences Building, Berkeley, CA 94720, USA

4 Department of Molecular and Cell Biology, Life Sciences Annex, University of California, Berkeley, CA 94720, USA

5 Department of Plant Biology, Edward R. Madigan Laboratory, University of Illinois, 1201 West Gregory Drive, Urbana, IL 61801, USA

6 DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA

7 Current address: Bio Architecture Lab Inc, 604 Bancroft Way, Berkeley, CA 94710, USA

8 Current address: Department of Plant Biology, University of Georgia, Athens, GA 30602, USA

9 Current address: The Procter & Gamble Company, Mason Business Center, 8700 Mason Montgomery Road Box 513, Mason, OH 45040-9462, USA

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BMC Genomics 2013, 14:864  doi:10.1186/1471-2164-14-864

Published: 9 December 2013

Abstract

Background

The Miscanthus genus of perennial C4 grasses contains promising biofuel crops for temperate climates. However, few genomic resources exist for Miscanthus, which limits understanding of its interesting biology and future genetic improvement. A comprehensive catalog of expressed sequences were generated from a variety of Miscanthus species and tissue types, with an emphasis on characterizing gene expression changes in spring compared to fall rhizomes.

Results

Illumina short read sequencing technology was used to produce transcriptome sequences from different tissues and organs during distinct developmental stages for multiple Miscanthus species, including Miscanthus sinensis, Miscanthus sacchariflorus, and their interspecific hybrid Miscanthus × giganteus. More than fifty billion base-pairs of Miscanthus transcript sequence were produced. Overall, 26,230 Sorghum gene models (i.e., ~ 96% of predicted Sorghum genes) had at least five Miscanthus reads mapped to them, suggesting that a large portion of the Miscanthus transcriptome is represented in this dataset. The Miscanthus × giganteus data was used to identify genes preferentially expressed in a single tissue, such as the spring rhizome, using Sorghum bicolor as a reference. Quantitative real-time PCR was used to verify examples of preferential expression predicted via RNA-Seq. Contiguous consensus transcript sequences were assembled for each species and annotated using InterProScan. Sequences from the assembled transcriptome were used to amplify genomic segments from a doubled haploid Miscanthus sinensis and from Miscanthus × giganteus to further disentangle the allelic and paralogous variations in genes.

Conclusions

This large expressed sequence tag collection creates a valuable resource for the study of Miscanthus biology by providing detailed gene sequence information and tissue preferred expression patterns. We have successfully generated a database of transcriptome assemblies and demonstrated its use in the study of genes of interest. Analysis of gene expression profiles revealed biological pathways that exhibit altered regulation in spring compared to fall rhizomes, which are consistent with their different physiological functions. The expression profiles of the subterranean rhizome provides a better understanding of the biological activities of the underground stem structures that are essentials for perenniality and the storage or remobilization of carbon and nutrient resources.

Keywords:
Transcriptome; Miscanthus; Illumina; Short read sequencing; RNA sequencing; Development