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Open Access Research article

Sequencing of transcriptomes from two Miscanthus species reveals functional specificity in rhizomes, and clarifies evolutionary relationships

Changsoo Kim1, Tae-Ho Lee14, Hui Guo1, Sung Jin Chung2, Andrew H Paterson1, Do-Soon Kim3 and Geung-Joo Lee2*

  • * Corresponding author: Geung-Joo Lee gjlee@cnu.ac.kr

  • † Equal contributors

Author Affiliations

1 Plant Genome Mapping Lab, University of Georgia, 111 Riverbend RD, Athens, GA 30602, USA

2 Department of Horticulture, Chungnam National University, Daejeon 305-764, South Korea

3 Department of Plant Science, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, South Korea

4 Present address: Genomics Division, National Academy of Agricultural Science, Rural Development Administration, Suwon 441-707, South Korea

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BMC Plant Biology 2014, 14:134  doi:10.1186/1471-2229-14-134

Published: 18 May 2014

Abstract

Background

Miscanthus is a promising biomass crop for temperate regions. Despite the increasing interest in this plant, limited sequence information has constrained research into its biology, physiology, and breeding. The whole genome transcriptomes of M. sinensis and M. sacchariflorus presented in this study may provide good resources to understand functional compositions of two important Miscanthus genomes and their evolutionary relationships.

Results

For M. sinensis, a total of 457,891 and 512,950 expressed sequence tags (ESTs) were produced from leaf and rhizome tissues, respectively, which were assembled into 12,166 contigs and 89,648 singletons for leaf, and 13,170 contigs and 112,138 singletons for rhizome. For M. sacchariflorus, a total of 288,806 and 267,952 ESTs from leaf and rhizome tissues, respectively, were assembled into 8,732 contigs and 66,881 singletons for leaf, and 8,104 contigs and 63,212 singletons for rhizome. Based on the distributions of synonymous nucleotide substitution (Ks), sorghum and Miscanthus diverged about 6.2 million years ago (MYA), Saccharum and Miscanthus diverged 4.6 MYA, and M. sinensis and M. sacchariflorus diverged 1.5 MYA. The pairwise alignment of predicted protein sequences from sorghum-Miscanthus and two Miscanthus species found a total of 43,770 and 35,818 nsSNPs, respectively. The impacts of striking mutations found by nsSNPs were much lower between sorghum and Miscanthus than those between the two Miscanthus species, perhaps as a consequence of the much higher level of gene duplication in Miscanthus and resulting ability to buffer essential functions against disturbance.

Conclusions

The ESTs generated in the present study represent a significant addition to Miscanthus functional genomics resources, permitting us to discover some candidate genes associated with enhanced biomass production. Ks distributions based on orthologous ESTs may serve as a guideline for future research into the evolution of Miscanthus species as well as its close relatives sorghum and Saccharum.

Keywords:
Miscanthus sinensis; Miscanthus sacchariflorus; Expressed sequence tags; Synonymous substitution; Orthologous sequences; Nonsynonymous SNPs