Table 1.
Quality metrics of Illumina sequencing analysis.
| (A) Total number of reads and read length before and after quality checking and trimming | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Bacteria | Fungi | |||||||||
| Total of raw reads before QC | 1548999 | 1778124 | ||||||||
| Average read length before QC | 502 | 602 | ||||||||
| Total of assigned reads after QC | 1394267 | 1490716 | ||||||||
| Average read length after QC | 395 ± 2 | 281 ± 5 | ||||||||
| (B) Assigned reads | Root | Stem | ||||||||
| DAR | DBR | QAR | QBR | DAS | DBS | QAS | QBS | |||
| Average of reads | Bacteria | 53475 ± 1450 | 56322 ± 1404 | 48375 ± 3773 | 51063 ± 2249 | 67138 ± 6984 | 65134 ± 7121 | 62827 ± 9335 | 60422 ± 7691 | |
| Fungi | 53942 ± 3031 | 43887 ± 2355 | 51022 ± 4673 | 47400 ± 2332 | 74984 ± 3683 | 72160 ± 4296 | 81699 ± 3088 | 71812 ± 1953 | ||
| Average read length | Bacteria | 398 ± 1 | 397 ± 1 | 396 ± 1 | 395 ± 1 | 394 ± 0 | 394 ± 0 | 394 ± 0 | 394 ± 0 | |
| Fungi | 272 ± 9 | 272 ± 8 | 283 ± 35 | 288 ± 6 | 291 ± 11 | 252 ± 9 | 299 ± 11 | 293 ± 4 | ||
| (C) Non-target rRNA (%) | ||||||||||
| Mitochondria Chloroplast/plastid | Bacteria | 0.05 ± 0.01 | 0.04 ± 0.01 | 0.02 ± 0.01 | 0.01 ± 0.01 | 0.02 ± 0.01 | 0.02 ± 0.01 | 0.03 ± 0.01 | 0.03 ± 0.01 | |
| Fungi | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ||
| Bacteria | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ||
| Fungi | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ||
| (D) Unclassified reads | ||||||||||
| Reads (%) | Bacteria | 0 | 0 | 0.03 ± 0.01 | 0 | 0.08 ± 0.04 | 0 | 0.36 ± 0.36 | 0 | |
| Fungi | 7.86 ± 3.99 | 4.80 ± 2.31 | 2.08 ± 1.34 | 1.04 ± 0.89 | 2.25 ± 0.98 | 11.38 ± 9.24 | 6.75 ± 3.26 | 8.38 ± 3.71 | ||
(A) Quality metrics before and after quality control (QC). The average read length was calculated based on 24 samples across all plant compartments. (B) The average number of assigned reads (±standard deviation) per plant compartment and the average length of assigned reads. Statistical differences at the 95% confidence interval are indicated with lowercase letters. DAR, Root of transgenic poplar in Daqing; DBR, Root of non-transgenic poplar in Daqing; QAR, Root of transgenic poplar in Qiqihar; QBR, Root of non-transgenic poplar in Qiqihar; DAS, Stem of transgenic poplar in Daqing; DBS, Stem of non-transgenic poplar in Daqing; QAS, Stem of transgenic poplar in Qiqihar; and QBS, Stem of non-transgenic poplar in Qiqihar. (C) Comparison of the number of non-target 16S rRNA and ITSs sequences (%) co-amplified during PCR amplification. (D) Reads that could not be unambiguously classified at the phylum level (“unclassified”) (%).