Table 1.
Biological materials, Primers and PCR conditions used for the reference datasets.
Figure 1.
Analysis of structure and variability of partial RPB1 genes in the longer reference dataset 1.
A 50-bp sliding window was used to generate (a) and (b). (a): Mean K2P distances of pairwise comparisons of the sequences: the mean K2P distances within the introns are higher than 6%, therefore they are outside the range of the x-axis. Consequently, the black lines indicate that the exons have a relatively low mean K2P distance. (b): the sum of diagnostic nucleotides along the alignment as analysed using SpideR. A higher number of diagnostic nucleotides indicate good separation of species. (c): corresponding intron-exon structure of partial RPB1, including primer binding sites within the alignment.
Figure 2.
RAxML phylogenetic tree based on the exon of the fragment RPB1-Ac and RPB1-DR1210.
Support values are from RAxML (1000 bootstrap replicates (BR)), MP (1000 BR), NJ (1000 BR) and MrBayes. * Sequences from this study, § Sequences contributed to Schoch et al. [39].
Figure 3.
Barcode gap analysis of the RPB1 fragment RPB1-Ac to RPB1-DR1210r, based on K2P distances.
Every sequence was plotted with its corresponding intraspecific variation and minimum interspecific variation. Bars indicate K2P difference between the maximum intraspecific (bottom) and minimum interspecific divergence (top) of each sequence. The red asterisk indicates sequences with small K2P distances of the three species Gigaspora rosea, Gi. gigantea and Gi. candida, which are not resolved. Two of these species are assumed to be conspecific. Colored bars represent sequences of the following species: apricot - Funneliformis mosseae, magenta – Rhizophagus irregularis, green – Rhizophagus clarus, red – Ambispora leptoticha. Bars touching zero at their lower end stand for species represented by a single sequence.
Figure 4.
Principal Coordinates Analysis of weighted UniFrac distances.
Figure 5.
Relative phylogenetic taxon distribution in the different treatments and plots.