Table 1.
Identification and comparison of special genera in the rhizospheric soil of the glyphosate-tolerant (GT) soy bean line N698 and its control MD12 by shotgun metagenomic approaches.
| Bioinformatics Tool | SOAPaligner | One Codex Data Platform | ||||
|---|---|---|---|---|---|---|
| Database | NCBI nucleotide database | One Codex DB | RefSeq DB | |||
| Sample name | MGMRh | MGNRh | MGMRh | MGNRh | MGMRh | MGNRh |
| Total mapped reads | 790,310 | 318,187 | 7,413,129 | 6,118,123 | 4,878,689 | 4,058,863 |
| Genus name | Mapped reads (proportions of total mapped reads) | |||||
| Rahnella 1 | 316,533 (40.052%) | 385 (0.1210%) | 363,110 (4.898%) | 510 (0.00834%) | 216,768 (4.443%) | 364 (0.00897%) |
| Serratia | 28,900 (3.657%) | 38 (0.0120%) | 36,565 (0.4932%) | 1416 (0.02314%) | 20,940 (0.4293%) | 1959 (0.04826%) |
| Yersinia 2 | 381 (0.0482%) | 6 (0.0019%) | 337 (0.0045%) | 37 (0.00060%) | 1144 (0.0234%) | 111 (0.00273%) |
| Variovorax 1 | 27,824 (3.521%) | 21,698 (6.819%) | 158,661 (2.1403%) | 150,119 (2.4537%) | 123,709 (2.536%) | 109,798 (2.7051%) |
| Ewingella 1 | ND | ND | 1077 (0.01453%) | 67 (0.00110%) | ND | ND |
| Ramlibacter 1 | 1846 (02336%) | 2518 (0.7913%) | 12,642 (0.1705%) | 17,414 (0.28463%) | 17,680 (0.3624%) | 23,159 (0.57058%) |
| Luteibacter 2 | 24 (0.0030%) | 2 (0.0006%) | 129,081 (1.7413%) | 9029 (0.14758%) | ND | ND |
| Pedobacter 2 | 638 (0.0807%) | 166 (0.0522%) | 29,399 (0.3966%) | 6812 (0.11134%) | 5210 (0.1068%) | 2026 (0.04991%) |
| Flavisolibacter 2 | 20 (0.0025%) | 19 (0.0060%) | ND | ND | ND | ND |
1 Genus detected by 16S rDNA V5–7 region amplicon deep sequencing only. 2 Genus detected by 16S rDNA V4 region amplicon deep sequencing only. 3 ND means “not detected”. MGMRh and MGNRh represent pooled rhizospheric DNA sample of MRh and NRh for shotgun metagenome sequencing, respectively.