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Figure 1. Violin plots of the average percentage of forward and reverse
reads that were merged to form contigs from each primer set (ITS1F/ITS2,
LROR/LR3 and LR22F/LR3). The number of total reads returned for each
dataset is listed above the boxes and the number of total (i.e. fungal
and non-fungal) OTUs found after filtering and quality control is given
below.
Figure 2. Primer set variation (ITS1F/ITS2, LROR/LR3, LR22F/LR3) in OTU
length and read number assigned to each OTU according to taxonomic
assignment by Kingdom and fungal phylum using the hybrid (for ITS1F) or
UTAX (for LSU) method (A, B) and the RDP classifier (C, D). Box plot
height and whiskers represent OTU length range, whereas the box plot
width represents the proportion of reads assigned to each group. The
LROR primer set was almost entirely comprised of forward reads with a
length of 283 bp, resulting in a flat line. SUPP FIG 4 contains
additional graphs of the LROR data separately. Percentages indicate the
proportion of non-fungal (A, C) and fungal (B, D) OTUs in each dataset.
Note that Glomeromycotina is a subphylum within the Mucoromycota but is
categorized separately for comparison with the ITS taxonomy.
Figure 3. Relative abundance of reads assigned to each phylum of early
diverging fungi by sample type for each primer set.
Figure 4. Non-metric multi-dimensional scaling (NMDS) ordination plots
for all fungi and early diverging fungal communities recovered by the
primer sets (ITS1F/ITS2, LROR/LR3, LR22F/LR3) for all California (CA)
and Florida (FL) environmental sampling sites. Point colors represent
different sampling locations and point shapes indicate primer set.
Stress values are listed for each dataset.
Figure 5. Comparison of alpha diversity measures for early diverging
fungi for each primer set by site (colors) and sample type (shapes).
Figure 6. Maximum likelihood phylogenetic reconstruction of fungal LSU
sequences including references from GenBank and newly sequenced isolates
from this study. 50 OTUs identified only as “Fungi” from each of the
LROR and LR22F datasets were included and the numbers are bolded.
Analyses were performed in RAxML v 8 using the GTR + GAMMA model and
1,000 bootstrap replicates. Classes of fungi are colored if they include
unknown LSU OTUs or shaded grey if they do not. The dark grey “BLAST
match to protists” shading indicates that these clades are comprised of
OTUs that had GenBank matches to protist sequences with the OTU IDs in
red. Asterisks indicate early diverging clades. SUPP TABLE 5 has a list
of all OTUs included in the phylogeny along with their BLAST matches.
Figure 7. Maximum likelihood phylogenetic reconstruction of
Zoopagomycota LSU sequences including references from GenBank and newly
sequenced isolates from this study. OTUs identified as Zoopagomycota
species from each of the LROR and LR22F datasets were included and the
numbers are bolded and include the order to which each OTU was
classified. Analyses were performed in RAxML v 8 using the GTR + GAMMA
model and 1,000 bootstrap replicates. Branch supports ≥70 are shown.
Table 1. Zoopagomycota mock community members and results of mock
community OTU taxonomy comparisons across the ITS1F/ITS2, LROR/LR3, and
LR22F/LR3 primer sets, including the target fragment length in base
pairs (bp), GenBank accession numbers (ITS, LSU), and the primer columns
list the number of OTUs of each mock community member detected by the
RDP classifier taxonomy (outside parentheses) versus the RDP+SILVA LSU
database (for LSU) or the AMPtk hybrid method (for ITS1F) (in
parentheses).