Tables, Figures and supplementary files

Table 1. Investigated dataset with details on the type of sample assembled for the analysis, the geographic origin and taxonomic identity of the samples; N = number of individuals (= DNA extracts) multiplexed (pooled) in each tube; n = number of individual DNA extracts per species.
Figure 1 A-B . Boxplots of length (A) and GC-content (B) of the 5S-IGS units in the referenceQuercus dataset (1160 sequences) and in each species.
Figure 2. Circular RAxML tree of the reference dataset. A: full tree with sections colored; B-D: only species of each section are colored.
Figure 3. Raw RAxML trees (unrooted) including references and HTS data of samples E5 (subset cut-off = 5) and E4 (subset cut-off = 2). Black leaves represent HTS reads; reference sequences are colored based on sections.
Figure 4. Comparison between BLAST and EPA assignments of HTS sequences with abundance >25 in each sample. Colors of the pie-sectors are according to the main 5S-IGS variants identified.
Figure 5. RAxML jplace tree including references and the EPA placements (in black) for a pure (F2) and a mixed (H1) samples with abundance cut-off = 25.
Figure 6. RAxML jplace tree including trees references and the EPA placements for the total HTS six samples with abundance > 25 (in red).