Open Access Research

Genomic and small RNA sequencing of Miscanthus × giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses

Kankshita Swaminathan12, Magdy S Alabady2, Kranthi Varala1, Emanuele De Paoli3, Isaac Ho4, Dan S Rokhsar45, Aru K Arumuganathan6, Ray Ming27, Pamela J Green38, Blake C Meyers3, Stephen P Moose12 and Matthew E Hudson12*

Author Affiliations

1 Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

2 Energy Biosciences Institute and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

3 Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA

4 DOE Joint Genome Institute, Walnut Creek, CA 94598, USA

5 Center for Integrative Genomics, University of California at Berkeley, Berkeley, CA 94720, USA

6 Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA

7 Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

8 College of Marine Studies, University of Delaware, Newark, DE 19711, USA

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Genome Biology 2010, 11:R12  doi:10.1186/gb-2010-11-2-r12

Published: 3 February 2010

Abstract

Background

Miscanthus × giganteus (Mxg) is a perennial grass that produces superior biomass yields in temperate environments. The essentially uncharacterized triploid genome (3n = 57, x = 19) of Mxg is likely critical for the rapid growth of this vegetatively propagated interspecific hybrid.

Results

A survey of the complex Mxg genome was conducted using 454 pyrosequencing of genomic DNA and Illumina sequencing-by-synthesis of small RNA. We found that the coding fraction of the Mxg genome has a high level of sequence identity to that of other grasses. Highly repetitive sequences representing the great majority of the Mxg genome were predicted using non-cognate assembly for de novo repeat detection. Twelve abundant families of repeat were observed, with those related to either transposons or centromeric repeats likely to comprise over 95% of the genome. Comparisons of abundant repeat sequences to a small RNA survey of three Mxg organs (leaf, rhizome, inflorescence) revealed that the majority of observed 24-nucleotide small RNAs are derived from these repetitive sequences. We show that high-copy-number repeats match more of the small RNA, even when the amount of the repeat sequence in the genome is accounted for.

Conclusions

We show that major repeats are present within the triploid Mxg genome and are actively producing small RNAs. We also confirm the hypothesized origins of Mxg, and suggest that while the repeat content of Mxg differs from sorghum, the sorghum genome is likely to be of utility in the assembly of a gene-space sequence of Mxg.