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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 .

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