Table 2.
Genes that are similarly responsive in the GLDTFt::5'truncatedNAC052 and the GLDTFt:NAC052 lines, but differently responsive in the activation-tagged line and the CRISPR/Cas line
| Gene ID | Gene description | Abbreviated gene name | Activation tagged | CRISPR/Cas | GLDT:: truncatedNAC052 | GLDT:: NAC052 | |
|---|---|---|---|---|---|---|---|
| 1 | AT1G01060 | LHY encodes a myb-related putative transcription factor (TF) involved in circadian rhythm along with another myb TF CCA1. | LHY | 2.06 | 2.37 | 0.5<FC<2.0 | 0.5<FC<2.0 |
| 2 | AT1G16730 | UNKNOWN PROTEIN 6, expressed during flowering stage, petal differentiation, and expansion stage; expressed in guard cell. | UP6 | 2.10 | 2.44 | 0.5<FC <2.0 | 0.5<FC<2.0 |
| 3 | AT4G40020 | Myosin heavy chain-related protein; involved in reciprocal meiotic recombination. | 3.34 | 2.37 | 0.5<FC<2.0 | 0.5<FC<2.0 | |
| 4 | AT5G05580 | Encodes a temperature-sensitive plastidic fatty acid desaturase. Located in chloroplast, expressed in guard cell. | FAD8 | 0.5<FC<2.0 | 0.5<FC<2.0 | 0.47 | 0.42 |
| 5 | AT5G67370 | CONSERVED IN THE GREEN LINEAGE; involved in response to iron ion starvation; located in chloroplast, integral component of membrane. | CGLD27 | 0.5<FC<2.0 | 0.5<FC<2.0 | 0.47 | 0.32 |
| 6 | AT1G72416 | Chaperone DnaJ-domain superfamily protein; located in cytoplasm, integral component of membrane; expressed in guard cell. | 0.5< FC <2.0 | 0.5< FC <2.0 | 0.44 | 0.45 | |
| 7 | AT2G34510* | Choice-of-anchor C domain protein, putative; expressed in cauline leaf, collective leaf structure, cotyledon. | 0.5<FC<2.0 | 0.5<FC<2.0 | 0.45 | 0.33 | |
| 8 | AT4G11460* | Encodes a cysteine-rich receptor-like protein kinase, involved in defence response to bacteria, protein phosphorylation. | CRK30 | 0.5<FC<2.0 | 0.5<FC<2.0 | 0.42 | 0.36 |
| 9 | AT5G01015* | Transmembrane protein. | 0.5<FC<2.0 | 0.5<FC<2.0 | 0.35 | 0.26 | |
| 10 | AT1G74010 | Calcium-dependent phosphotriesterase superfamily protein; located in cytosol, endoplasmic reticulum, extracellular region, membrane, plant-type cell wall. | 0.5<FC<2.0 | 0.5<FC<2.0 | 2.13 | 5.03 | |
| 11 | AT2G22880 | VQ motif-containing protein; involved in response to UV-B; located in nucleus. | VQ12 | 0.5<FC<2.0 | 0.5<FC<2.0 | 2.52 | 9.60 |
| 12 | AT2G39350 | Belongs to a clade of five Arabidopsis thaliana ABCG half-transporters that are required for synthesis of an effective suberin barrier in roots and seed coats (ABCG2, ABCG6, and ABCG20) and for synthesis of an intact pollen wall (ABCG1 and ABCG16). | ABCG1 | 0.5<FC<2.0 | 0.5<FC<2.0 | 2.71 | 7.97 |
| 13 | AT2G39980 | HXXXD-type acyl-transferase family protein; involved in response to karrikin; has transferase activity. | 0.5<FC<2.0 | 0.5< FC <2.0 | 2.17 | 3.71 | |
| 14 | AT4G06410 | Natural antisense transcript overlaps with AT4G16670. | 0.5<FC<2.0 | 0.5<FC<2.0 | 2.28 | 5.53 | |
| 15 | AT4G15550 | IAGLU, INDOLE-3-ACETATE BETA-d-GLUCOSYLTRANSFERASE. | IAGLU | 0.5< FC <2.0 | 0.5< FC <2.0 | 2.58 | 2.51 |
| 16 | AT4G25810* | Xyloglucan endotransglycosylase-related protein (XTR6); involved in cell wall biogenesis, cell wall organization, xyloglucan metabolic process; located in Golgi apparatus, apoplast, cell wall, extracellular region. | XTR6 | 0.5<FC<2.0 | 0.5<FC<2.0 | 2.00 | 5.71 |
| 17 | AT4G35770 | Senescence-associated gene that is strongly induced by phosphate starvation. Transcripts are differentially regulated at the level of mRNA stability at different times of day. | SEN1 | 0.5<FC<2.0 | 0.5<FC<2.0 | 2.09 | 2.66 |
| 18 | AT5G13330* | Encodes a member of the ERF (ethylene response factor) subfamily B-4 of ERF/AP2 transcription factor family. | Rap2.6L | 0.5<FC<2.0 | 0.5<FC<2.0 | 2.12 | 4.55 |
| 19 | AT1G75450 | This gene used to be called AtCKX6. It encodes a protein whose sequence is similar to cytokinin oxidase/dehydrogenase. | CKX5 | 0.50 | 0.30 | 2.00 | 2.65 |
| 20 | AT2G19800 | Encodes a myo-inositol oxygenase family gene, involved in l-ascorbic acid biosynthetic process, inositol catabolic process, oxidation–reduction process, syncytium formation. | MIOX2 | 0.36 | 0.50 | 2.00 | 2.30 |
| 21 | AT3G50970 | Belongs to the dehydrin protein family, involved in cold acclimation, defence response to fungus, response to abscisic acid, response to cold, response to water, response to water deprivation; the mRNA is cell-to-cell mobile. | LTI30 | 0.28 | 0.46 | 2.00 | 3.23 |
| 22 | AT4G20970 | Basic helix–loop–helix (bHLH) DNA-binding superfamily protein; has DNA-binding transcription factor activity. | 0.39 | 0.42 | 2.00 | 2.00 | |
| 23 | AT4G21650* | Subtilase family protein; involved in proteolysis. | SBT3.13 | 0.36 | 0.48 | 2.00 | 2.00 |
| 24 | AT5G07000 | Encodes a member of the sulfotransferase family of proteins. It may be able to act on structurally related jasmonates. | ST2B | 0.41 | 0.23 | 0.5<FC<2.0 | 0.5<FC<2.0 |
| 25 | AT5G55250 | Encodes an enzyme that specifically converts IAA to its methyl ester form MelIAA, involved in auxin homeostasis, methylation, polarity specification of adaxial/abaxial axis. | IAMT1 | 0.47 | 0.34 | 0.5<FC<2.0 | 0.5<FC<2.0 |
| 26 | AT1G04220 | Encodes KCS2, a member of the 3-ketoacyl-CoA synthase family involved in the biosynthesis of VLCFA (very long chain fatty acids). | KCS2 | 0.5<FC<2.0 | 0.5<FC<2.0 | 2.16 | 3.01 |
| 27 | AT1G64660 | Encodes a functional methionine gamma-lyase, a cytosolic enzyme catalyses the degradation of methionine into methanethiol, alpha-ketobutyrate, and ammonia. | MGL | 0.5<FC<2.0 | 0.5<FC<2.0 | 2.05 | 3.26 |
| 28 | AT2G23170 | Encodes an IAA-amido synthase that conjugates Asp and other amino acids to auxin in vitro. | GH3.3 | 0.5<FC<2.0 | 0.5<FC<2.0 | 2.57 | 4.20 |
| 29 | AT3G54400* | Eukaryotic aspartyl protease family protein; involved in protein catabolic process, proteolysis; located in apoplast, cell wall, chloroplast, extracellular region, plant-type cell wall. | 0.5<FC<2.0 | 0.5<FC<2.0 | 2.12 | 4.24 | |
| 30 | AT3G55500 | Expansin-like protein, involved in plant-type cell wall loosening, plant-type cell wall modification involved in multidimensional cell growth, plant-type cell wall organization, syncytium formation, unidimensional cell growth. | ExPA16 | 0.5<FC<2.0 | 0.5<FC<2.0 | 2.01 | 2.54 |
| 31 | AT3G62090 | PHYTOCHROME-INTERACTING FACTOR 6, encodes a novel Myc-related bHLH transcription factor, which physically associated with APRR1/TOC1 and is a member of PIF3 transcription factor family. | PIL2 | 0.5<FC<2.0 | 0.5<FC<2.0 | 2.06 | 2.27 |
| 32 | AT5G06570* | Alpha/beta-Hydrolase superfamily protein; expressed during petal differentiation and expansion stage. | 0.5<FC<2.0 | 0.5<FC<2.0 | 2.16 | 7.02 | |
| 33 | AT2G32990 | Glycosyl hydrolase 9B8; involved in cell wall organization, cellulose catabolic process. | GH9B8 | 0.45 | 0.40 | 0.5<FC<2.0 | 0.5<FC<2.0 |
Fold changes are compared with the reference line. Gene IDs in bold are involved in cell wall organization; gene IDs that include ‘*’ overlap with up-regulated genes after NAC050/052-RNAi (Ning et al., 2015); gene IDs underlined overlap with differentially expressed genes between total leaf and bundle sheath only (Aubry et al., 2014); fold changes in blue are increased compared with the reference line (P=0.05); fold changes in red are decreased compared with the reference line (P=0.05).