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Table 1 Quality metrics of pyrosequencing analysis

From: Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees

A. Total number of reads and read length before and after quality checking and trimming
Total # of raw reads before QC 341,915
Average read length before QC 405 ± 96
Total # of assigned reads after QC 204,723
Average read length after QC 207 ± 4
B. Assigned reads Rhizosphere soil Root Stem Leaf
Average # of reads 5058 ± 615 5311 ± 643 2761 ± 1174 3034 ± 960
Singletons (%) 26.09 ± 0.01a 5.01 ± 0.55b 2.60 ± 0.35b 2.21 ± 0.65b
Normalization to 2000 reads per sample
C. Non-target rRNA (%) Rhizosphere soil Root Stem Leaf
Chloroplast/plastid 0 0.01 ± 0.01 0.44 ± 0.17 0.03 ± 0.02
Mitochondria 0 0 0 0
Archaea 0.03 ± 0.01 0 0 0
D. Unclassified reads Rhizosphere soil Root Stem Leaf
Reads (%) 34.07 ± 1.10a 4.74 ± 0.32b 19.05 ± 4.32b 3.59 ± 1.03b
  1. A: Quality metrics before and after quality control (QC), the average read length was calculated based on 52 samples across all plant compartments. B: Average number of assigned reads (± standard deviation) per plant compartment and percentages of singleton reads (± standard deviation). Numbers of singletons were statistically compared using one-way ANOVA and Tukey’s Honest significant differences post hoc tests. Statistical differences at the 95% confidence interval are indicated with lowercase letters. C: Comparison of the number of non-target 16S rRNA sequences (%) co-amplified during PCR amplification. and D: Reads that could not be unambiguously classified at the phylum level (“unclassified”) (%). Each plant compartment is evaluated separately and data represent 15 biologically independent replicates (± standard deviation) for the rhizosphere soil and root endosphere samples and 11 biologically independent replicates (± standard deviation) for the stem and leaf endosphere samples