File S1 - Multiple ITS Copies Reveal Extensive Hybridization within Rheum (Polygonaceae), a Genus That Has Undergone Rapid Radiation

Figure S1, The phylogenetic trees reconstructed using maximum likelihood method on a basis of nrDNA ITS1 (left) and ITS2 matrix (right), respectively. Bootstrap support values from ML analyses using PHYML are given below branches and the corresponding Bayesian posterior probabilities from Bayesian analyses using MrBayes are shown above branches. Figure S2, The phylogenetic trees reconstructed using maximum likelihood method on a basis of nrDNA ITS matrix including extra sequences from more individuals. Bootstrap support values from ML analyses using PHYML are given below branches and the corresponding Bayesian posterior probabilities from Bayesian analyses using MrBayes are shown above branches. The letter (X, Y, Z) after the species name present different individuals, and the numbers mean clone order. Table S1, Plant materials and list of accession numbers for the taxa used in the present study. The intron of trnK includes the matK gene and non-coding segments; rbcL-accD and trnL-F are intergenic spacers. Table S2, The frequency of two versions from all positive clones per Rheum species within 2-3 individuals. Table S3, GC content of ITS regions, the character of 5.8 S and ITS2 of Rheum species. Rumex crispus ITS region was used as reference. a present sharing three conserved motifs (motif 1: 5′-CGATGAAGAACGTAGC-3′, motif 2: 5′-GAATTGCAGAATCC-3′ and motif 3: 5′-TTTGAACGCA-3′); b present a stem hybridization; c present homologous structure existed. (DOC)