Table 1.
Samples and their ITS2 Genbank accession numbers included in this study.
Fig 1.
The predicted ITS2 secondary structure of the “Mu tong” taxa.
(a) Consensus secondary structure model of the ITS2 region based on 30 sequences covering four families (Actinidiaceae, Aristolochiaceae, Lardizabalaceae and Ranunculaceae). The four helices, each with a stem–loop, are labeled I–IV. Compatible base pairs are colored and the degree of conservation over the whole alignment is indicated with different degrees of color saturation. (b) One of the example secondary structures of Akebia quinata. (c) The position of the strictly conserved base pair sites (highlight in blue circle) found in the 70% consensus ITS2 secondary structure model.
Fig 2.
Comparison of multiple sequence alignments from different methods.
a. alignment from MARNA with secondary structure guiding; b. alignment from Clustal X without secondary structure guiding.
Table 2.
Statistics of phylogenetic analysis from different alignments.
Fig 3.
Comparison of MP trees inferred from sequences with different align methods.
a. MP tree inferred from sequence alignment by Clustal X; b. MP tree inferred from sequence alignment by secondary structure information. Numbers on the branches indicate the bootstrap values of MP above 50%, numbers following a species name represent individual numbers.
Fig 4.
Comparison of MP trees inferred from different data sets.
a. MP tree inferred from secondary structure coding information; b. MP tree inferred from the combined nucleotide sequences and secondary structure information. Numbers on the branches indicate the bootstrap values of MP above 50%, numbers following a species name represent individual numbers.