Table 5.
Expression of highly differentially expressed genes (DEGs; fold-change > 4, FDR < 0.001) involved in photosynthesis and photorepair identified in Karlodinium veneficum treated with a combination of putrescine and ammonium (Both). Con., control; NH4, ammonium; Putr., putrescine. Gene expression was measured as TPM (transcripts per million) and normalized using the TMM (trimmed mean of M values) method, generated by Salmon (v0.11.2) [53] and embedded in Trinity (v2.8.5) [54,55]. ChlM, magnesium-protoporphyrin IX methyltransferase; FCP, fucoxanthin-chlorophyll a-c binding protein; PP264, protein LOW PHOTOSYNTHETIC EFFICIENCY 1; PAPP5, Serine/threonine-protein phosphatase 5; ChlH, magnesium-chelatase subunit ChlH; DEGP2, protease Do-like 2. SOD, superoxide dismutase. Asterisk “*” indicates the gene was also identified as a DEG in K. veneficum treated with putrescine alone. Sequences are listed in Supplementary File S5.
| Transcript ID | Gene Description | Normalized Gene Expression (TMM) | |||
|---|---|---|---|---|---|
| Con. | NH4 | Putr. | Both | ||
| DN124564_c0_g1_i1 | ChlM | 1.85 | 0.46 | 2.38 | 0.00 |
| DN154913_c0_g1_i1 | FCP | 1.89 | 0.80 | 2.50 | 0.00 |
| DN133788_c0_g1_i1 | Pheophorbide a oxygenase | 3.77 | 4.95 | 4.52 | 0.00 |
| DN101633_c0_g1_i1 | PP264 (PP264_1) | 7.15 | 5.02 | 3.15 | 0.00 |
| DN152556_c0_g1_i1 | PP264 (PP264_2) | 3.71 | 6.08 | 3.81 | 0.00 |
| DN97632_c0_g1_i1 | PP264 (PP264_3) | 2.77 | 6.00 | 0.57 | 0.00 |
| DN68599_c0_g1_i1 | PP264 (PP264_4) | 14.75 | 6.70 | 4.66 | 1.18 |
| DN99820_c0_g1_i1 | PAPP5 | 3.41 | 2.76 | 2.47 | 0.00 |
| DN128516_c0_g1_i1 | UVR8 (UVR8_1) | 2.18 | 4.28 | 8.94 | 0.00 |
| DN37485_c0_g1_i1 | UVR8 (UVR8_2) | 5.31 | 2.96 | 1.07 | 0.45 |
| DN12312_c0_g1_i1 | ChlH (ChlH1) | 21.42 | 21.39 | 10.34 | 1.02 |
| DN14809_c0_g1_i1 | ChlH (ChlH2) | 19.58 | 16.31 | 10.22 | 1.15 |
| DN12312_c0_g2_i1 | ChlH (ChlH3) | 28.43 | 20.67 | 15.23 | 2.58 |
| DN28119_c0_g1_i1 | ChlH (ChlH4) | 30.15 | 30.44 | 14.03 | 3.78 |
| DN8652_c0_g2_i1 | ChlH (ChlH5) | 45.86 | 56.98 | 22.30 | 5.04 |
| DN37694_c0_g1_i2 | DEGP2 | 0.72 | 0.53 | 2.89 | 6.38 |
| DN143715_c0_g1_i1 | SOD | 0.00 | 0.71 | * 3.53 | 2.45 |