10 | FIGURE HEADINGS
Figure 1: Schematic depiction of CRABS workflow and
incorporated features. The five CRABS modules are indicated in blue.
CRABS implemented functions within each module are underlined.
Figure 2: CRABS generated reference database exploration
through CRABS incorporated visualizations. (a) horizontal bar graph
displaying number of species (blue) and number of sequences (orange)
contained within each class from the MiFish-E/U reference database. (b)
Bar graph displaying the proportion of base occurrence for the
primer-binding regions of the Taberlet c/h primer set, with base ‘A’
indicated by orange, base ‘C’ indicated in green, base ‘G’ indicated in
yellow, and base ‘T’ indicated in red. Degenerate bases (label ‘other’)
are indicated in grey. Sequences of the Taberlet c/h primer set are
presented on the bottom of the figure. (c) A phylogenetic tree depicting
the variation observed within the mlCOIintF/jgHC02198 amplicon region
for the genus Apteryx (kiwi). (d) Amplicon length distribution of the
gITS7/ITS4 primer set, with the overall amplicon length distribution
shaded grey and most abundant phyla represented by coloured lines
(Ascomycota: blue; Basidiomycota: orange; Mucoromycota: green). Figures
are taken straight from CRABS output without further editing.
Figure 3: Reference database comparison between CRABS (blue),
ecoPCR (purple), MetaCurator (green), RESCRIPt (yellow) for the (a)
MiFish-E/U, (b) Taberlet c/h, (c) mlCOIintF/jgHC02198, and (d)
gITS7/ITS4 primer sets. Number of sequences are depicted on the primary
y-axis and number of species are depicted on the secondary y-axis.
Figure 4: Venn diagrams displaying the proportional overlap of
species and identical sequences between CRABS (blue), ecoPCR (purple),
MetaCurator (green), and RESCRIPt (yellow) for the (a) MiFish-E/U, (b)
Taberlet c/h, (c) mlCOIintF/jgHC02198, and (d) gITS7/ITS4 primer sets.
Percentage values between brackets indicate the proportion of species
and identical sequences incorporated into the specific reference
database for each of the four software programs.
Figure 5: Observed differences in proportion of OTUs classified
between reference databases created by CRABS, ecoPCR, MetaCurator, and
RESCRIPt for the (a) MiFish-E/U, (b) Taberlet c/h, (c)
mlCOIintF/jgHC02198, and (d) gITS7/ITS4 primer sets. Taxonomy assignment
of OTUs was performed through the SINTAX algorithm implemented in
VSEARCH. Proportion of unassigned OTUs is indicated in black, species in
dark blue, genus in light blue, family in dark red, order in light red,
class in dark purple, phylum in light purple, and kingdom in green.
Figure 6: Venn diagrams displaying the proportional overlap in
taxonomy assignment of OTUs between CRABS (blue), ecoPCR (purple),
MetaCurator (green), RESCRIPt (yellow) for the (a) MiFish-E/U, (b)
Taberlet c/h, (c) mlCOIintF/jgHC02198, and (d) gITS7/ITS4 primer sets.