Fig. 2: Testing metabarcoding methods for amplification bias using community standards. | Nature Communications

Fig. 2: Testing metabarcoding methods for amplification bias using community standards.

From: VESPA: an optimized protocol for accurate metabarcoding-based characterization of vertebrate eukaryotic endosymbiont and parasite assemblages

Fig. 2

a Schematic overview of EukMix creation via 18S isolation and cloning. b Equimolar EukMix (left panel) and Log EukMix (right panel) community standard metabarcoding across primer sets (columns, labels at top and bottom) as compared to theoretical input (leftmost columns, gray boxes) shown as % abundance of reads per organism corresponding to bubble area. Any organism not detected (0 reads after quality filtering) is shown as a red X. See Supplementary Table 3 for parasite sources and strains. Bottom half of panels shows box plots of mean fold difference from theoretical input of three replicates ± standard error of the mean (SEM) in which the central line is the median, box limits indicate first to third quartile range, and whiskers display minimum and maximum values. P values are derived from two-tailed Wilcoxon matched-pairs signed rank tests. ns, not significant. See Supplementary Table 5 for exact P-values. c Pearson correlation coefficients for the relationship between theoretical and observed read abundances for Equimolar EukMix (top) and Log EukMix (bottom). Primer set Owens 29F recovered the underlying communities most accurately (shading). Source data are provided as a Source Data file.

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