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

Additional files

Additional file 1:

Tabulations of Miscanthus×giganteus reads mapped to Sorghum and Rank Product analysis.

Format: ZIP Size: 15.5MB Download file

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Additional file 2:

Expression analysis of Spring versus Fall Rhizomes of Miscanthus×giganteus.

Format: XLSX Size: 7.6MB Download file

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Additional file 3:

KEGG and GO term enrichment analysis of Miscanthus×giganteus Spring versus Fall Rhizomes.

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Additional file 4:

A chimeric sequence generated by PCR in Miscanthus sinensis ‘IGR-2011-001’ 51 bases of the Sb01g001670 sequence showing a single chimeric clone, likely generated during the polymerase chain reaction. Variations in the first part of the chimera match paralog II (indicated by grey arrows) while the latter part match paralog I (indicated by black arrows). The purple line shows a 103 bp region between the SNPs at positions 164 and 268, which is 100% identical in both paralogs.

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Additional file 5:

Top 20 gene ontology terms in the 3 categories in the assembled Miscanthus transcripts.

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Additional file 6:

Characterization of Miscanthus contigs that match the plant repeat database.

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Additional file 7:

Sample collection and sequencing details.

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Additional file 8:

Primers used to verify gene expression and transcript assemblies.

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