Table 6.
Details of differentially expressed genes obtained from three different RNA seq experiments at FDR 0.01 at three different fold change settings
| HSB vs LSB | LST vs LSB | HST vs HSB | |||||||
|---|---|---|---|---|---|---|---|---|---|
| Fold change | Fold change | Fold change | |||||||
| ≥2 | ≥10 | <2 | ≥2 | ≥10 | <2 | ≥2 | ≥10 | <2 | |
| SoGI- DGE | (34476) SuSy 2 SuT2 |
(1723) SuSy 2 SuT2 |
(7) | (30809) SuSy 2 SuT2 |
(3279) SuSy 2 SuT |
(5) | (31) | (5) PAL CHS CCoAR |
– |
| SUGIT- DGE | (18543) SuSy 2 SuT2a |
(952) SuSy 2 SuT2a |
(2) | (11716) SuSy 2 SuT2 |
(872) SuSy 2 SuT3 |
(2) | (21) | (3) TC |
– |
| SAS-DGE | (20487) SuSy 2 SuT3 |
(575) | (4) | (19808) SuSy 2 SuT2 |
(1706) SuSy 1 SuT3 SWEET3 SPS1 |
(2) | (2826) | (74+) (3-) FE, LAC, BE |
(794+) (172-) SPP2 SWEET3 SWEET16 SPT |
SuSy-sucrose synthase; SuT-sucrose transporter; SWEET-bidirectional sugar transporter sweet; FL-Ferruloyl esterase; LAC-laccase; BE-beta expansin; SPP-sucrose phosphate phosphatase; SPT-sugar phosphate phosphate translocator; HSB, high sugar bottom internode; HST, high sugar top internode; LSB-low sugar bottom internode; LST-low sugar top internode; SoGI-Saccharum officinarum gene indices; SUGIT-Sugarcane Iso-Seq transcriptome database; SAS-sugarcane assembled sequences. The numbers in brackets indicate the number of DEGs obtained at that fold change setting, while the sucrose and sugar related genes within the DEGs are indicated below them. (+) and (−) denote upregulation and down regulation respectively. The genes in bold letters are present in all the three DEGs