Fig. 1

Plastid contamination across host plant species is driven by variation in host plastid V4 sequence. a Root microbiota were characterized from 32 angiosperm species using universal pPNA during PCR. b Plastid contamination with universal pPNA (light green bars) significantly varied across species (Likelihood ratio test χ² = 108, p < 0.001), but was consistently elevated in the Asteraceae (red shading). Note that bars are not stacked for host species amplified with both universal and modified pPNA. Each bar depicts the mean contamination rate observed with the respective pPNAs (e.g. Symphyotrichum ericoides exhibits a mean plastid contamination of 25% and 94% with the universal and modified pPNAs, respectively). c Members of the Asteraceae exhibit a single nucleotide mismatch compared to the universal pPNA sequence (shown below the multiple sequence alignment Original V4 pPNA). Amplified with a modified pPNA (shown below the multiple sequence alignment Asteraceae V4 pPNA), plastid contamination was reduced in Asteraceae host species (ANOVA F_5,1 = 31.07, p = 0.003), and elevated in non-Asteraceae host species (dark green bars ANOVA F_2,1 = 23.42, p = 0.04). We further tested whether single nucleotide mismatches in chloroplast V4 sequence leads to elevated plastid contamination rates by characterizing the root microbiome of Rhexia virginica (blue shading). This species belongs to the Melastomataceae, a lineage predicted to exhibit elevated plastid contamination due to an independent nucleotide substitution in chloroplast V4 sequence (see Fig. 2)