Table 1.
Whole transcriptomics of NTSR and HS blackgrass shoot tissue. Number of transcripts (contiguous sequences) in each functional category (BIN) is indicated for up and down regulation. (a) Mapping onto the NTSR or HS transcriptome assembly; (b) % of upregulated contigs relative to the number mapped onto the transcriptome; (c) fold changes across all functional categories following normalization
| BIN code | BIN name | (a) Contig expression | (b) Contig mapping | (c) Expression versus mapping | ||||
|---|---|---|---|---|---|---|---|---|
| Upregulated in NTSR | Upregulated in HS | All NTSR | All HS | % mapped in NTSR versus HS | % NTSR up‐reg contigs (# NTSR mapped contigs) | % HS up‐reg contigs (# HS mapped contigs) | ||
| 1 | Photosynthesis | 739 | 143 | 15 164 | 2978 | 83.6 | 4.9 | 4.8 |
| 2 | Major CHO metabolism | 7 | 23 | 650 | 252 | 72.1 | 1.1 | 9.1 |
| 3 | Minor CHO metabolism | 10 | 49 | 718 | 328 | 68.6 | 1.4 | 14.9 |
| 4 | Glycolysis | 13 | 10 | 979 | 298 | 76.7 | 1.3 | 3.4 |
| 5 | Fermentation | 1 | 3 | 90 | 42 | 68.2 | 1.1 | 7.1 |
| 6 | Gluconeogenesis | 2 | 0 | 100 | 39 | 71.9 | 2.0 | 0.0 |
| 7 | OPP | 3 | 3 | 288 | 92 | 75.8 | 1.0 | 3.3 |
| 8 | TCA/org. transformation | 29 | 10 | 813 | 287 | 73.9 | 3.6 | 3.5 |
| 9 | Mitochondrial electron transport/ATP synthesis | 5 | 3 | 294 | 116 | 71.7 | 1.7 | 2.6 |
| 10 | Cell wall | 12 | 37 | 936 | 455 | 67.3 | 1.3 | 8.1 |
| 11 | Lipid metabolism | 33 | 30 | 1485 | 663 | 69.1 | 2.2 | 4.5 |
| 12 | N‐metabolism | 21 | 3 | 734 | 168 | 81.4 | 2.9 | 1.8 |
| 13 | Amino acid metabolism | 61 | 37 | 2121 | 723 | 74.6 | 2.9 | 5.1 |
| 14 | S‐assimilation | 8 | 0 | 118 | 25 | 82.5 | 6.8 | 0.0 |
| 15 | Metal handling | 13 | 5 | 206 | 74 | 73.6 | 6.3 | 6.8 |
| 16 | Secondary metabolism | 46 | 17 | 1189 | 446 | 72.7 | 3.9 | 3.8 |
| 17 | Hormone metabolism | 33 | 42 | 867 | 482 | 64.3 | 3.8 | 8.7 |
| 18 | Cofactor and vitamin metabolism | 14 | 9 | 425 | 170 | 71.4 | 3.3 | 5.3 |
| 19 | Tetrapyrrole synthesis | 40 | 11 | 997 | 204 | 83.0 | 4.0 | 5.4 |
| 20 | Stress | 27 | 40 | 1193 | 595 | 66.7 | 2.3 | 6.7 |
| 21 | Redox | 24 | 25 | 1084 | 377 | 74.2 | 2.2 | 6.6 |
| 22 | Polyamine metabolism | 1 | 3 | 69 | 44 | 61.1 | 1.4 | 6.8 |
| 23 | Nucleotide metabolism | 5 | 17 | 481 | 251 | 65.7 | 1.0 | 6.8 |
| 24 | Biodegradation of xenobiotics | 1 | 0 | 91 | 34 | 72.8 | 1.1 | 0.0 |
| 25 | C1‐metabolism | 40 | 5 | 624 | 122 | 83.6 | 6.4 | 4.1 |
| 26 | Miscellaneous | 114 | 78 | 1926 | 937 | 67.3 | 5.9 | 8.3 |
| 27 | RNA | 22 | 177 | 3101 | 1943 | 61.5 | 0.7 | 9.1 |
| 28 | DNA | 3 | 27 | 749 | 413 | 64.5 | 0.4 | 6.5 |
| 29 | Protein | 81 | 270 | 11 139 | 5043 | 68.8 | 0.7 | 5.4 |
| 30 | Signalling | 33 | 152 | 2438 | 1543 | 61.2 | 1.4 | 9.9 |
| 31 | Cell | 20 | 67 | 2193 | 1132 | 66.0 | 0.9 | 5.9 |
| 32 | ‘micro RNA, natural antisense etc.’ | 0 | 0 | 1 | 0 | 100.0 | 0.0 | n/a |
| 33 | Development | 18 | 39 | 1036 | 631 | 62.1 | 1.7 | 6.2 |
| 34 | Transport | 58 | 84 | 3343 | 1517 | 68.8 | 1.7 | 5.5 |
| 35 | Not assigned | 176 | 246 | 232 305 | 82 444 | 73.8 | 0.1 | 0.3 |
| Total: | 290 946 | 119 240 | ||||||