Phylogenetic analysis of Miscanthus × giganteus ( Mxg ) based on nuclear ribosomal DNA. (a) Sites of variation in a nucleotide alignment of the ITS1, 5.8S and the ITS2 regions of the rDNA from various Miscanthus species and Mxg survey reads. Reads from the Mxg genome survey that matched the internal transcribed spacers (ITS1 and ITS2) and the 5.8S rRNA were manually aligned using Sequencher and McClade to Miscanthus, Maize, sorghum and Saccharum sequences from GenBank and variable residues identified. (b) Phylogenetic tree of Mxg survey reads together with related species. A Bayesian phylogenetic analysis of the residues from a 150-bp region of ITS2 spanned by several complete reads from Mxg and shown in bold in (a) was performed using the general time reversible (GTR) model of substitution and a gamma distribution of the rates of substitutions. Parameters estimated from the last 5,000 trees were used to calculate a posterior probability at each node and draw a 50% majority rule consensus tree (b). The numbers at the nodes indicate the percentage confidence in the branches as assessed using the posterior probabilities. The diamonds represent the individual Mxg survey reads from this region.