Table 6.
Enriched functional classes among differentially expressed genes in sak1 during 1O2 acclimation
| Primary Mapman class | Secondary Mapman class | Gene ID (v4) | Gene name | Annotation |
|---|---|---|---|---|
| Up-regulated genes | ||||
| Secondary metabolism | isoprenoids | Cre13.g565650.t1.1 | Geranylgeranyl pyrophosphate synthase/Polyprenyl synthetase | |
| Cre06.g267600.t1.1 | Lycopene epsilon cyclase | |||
| Cre09.g407200.t1.1 | Phytoene desaturase | |||
| Cre06.g267600.t1.1 | Lycopene epsilon cyclase | |||
| Cre01.g011100.t1.1 | Prenyltransferase and squalene oxidase repeat, Oxidosqualene-lanosterol cyclase and related proteins | |||
| N misc | Cre08.g381707.t1.1 | NF* | ||
| phenylpropanoids | Cre03.g207800.t1.1 | Alcohol dehydrogenase, class V | ||
| Cre14.g623650.t1.1 | Alcohol dehydrogenase, class V (Zinc-binding) | |||
| Cre01.g039350.t1.1 | Cytochrome P450 reductase, possibly CYP505B family | |||
| sulfur-containing | Cre06.g299400.t1.1 | NF* | ||
| wax | Cre17.g722150.t1.1 | PKS3 | Type III polyketide synthase | |
| Cre07.g318500.t1.2 | FAE1/Type III polyketide synthase-like protein, Chalcone and stilbene synthases | |||
| Lipid metabolism | ‘exotics’ (steroids, squalene etc) | Cre01.g061750.t1.1 | serine palmitoyltransferase | |
| Cre02.g137850.t1.1 | NF* | |||
| Cre83.g796250.t1.1 | NF* | |||
| Cre01.g011100.t1.1 | Prenyltransferase and squalene oxidase repeat, Oxidosqualene-lanosterol cyclase and related proteins | |||
| FA synthesis and FA elongation | Cre06.g256750.t1.1 | Acyl carrier protein thioesterase | ||
| Cre03.g182050.t1.1 | Long-chain acyl-CoA synthetases (AMP-forming) | |||
| Cre02.g074650.t1.1 | Kelch repeat-containing proteins, Acyl-CoA binding protei | |||
| glycerol metabolism | Cre01.g053000.t1.1 | GPD2 | Glycerol-3-phosphate dehydrogenase/dihydroxyacetone-3-phosphate reductase | |
| glycolipid synthesis | Cre13.g583600.t1.1 | DGD1 | Digalactosyldiacylglycerol synthase | |
| lipid degradation | Cre01.g057450.t1.2 | NF* | ||
| Cre02.g126050.t1.1 | NF* | |||
| phospholipid synthesis | Cre06.g281250.t1.1 | CFA1 | Cyclopropane fatty acid synthase | |
| Cre01.g038250.t1.1 | SDC1 | Serine decarboxylase | ||
| Cre11.g472700.t1.1 | NF* | |||
| Cre13.g604700.t1.2 | CDP-alcohol phosphatidyltransferase/Phosphatidylglycerol-phosphate synthase | |||
| Cell | vesicle transport | Cre18.g744100.t1.1 | NF* | |
| Cre17.g721900.t1.1 | COG5 | Component of oligomeric golgi complex | ||
| Cre01.g003050.t1.1 | SEC8 | Component of the Exocyst Complex | ||
| Cre04.g224800.t1.1 | Endosomal R-SNARE protein, Vamp7/Nyv1-family | |||
| Cre17.g728150.t1.1 | Endosomal R-SNARE protein, Yky6-family | |||
| Cre12.g507450.t1.1 | Trans-Golgi network Qa-SNARE protein, Syntaxin16/Syx16/Tlg2/Syp4-family | |||
| Cre03.g210600.t1.1 | NF* | |||
| Cre04.g225900.t1.1 | Endosomal R-SNARE protein, Vamp7/Nyv1-family | |||
| Cre02.g101400.t1.1 | CHC1 | Clathrin Heavy Chain | ||
| Cre17.g709350.t1.1 | Late endosomal Qc-SNARE protein, Syx8/Syntaxin8-family | |||
| Cre07.g342050.t1.1 | Endosomal Qb-SNARE, Npsn-family | |||
| Cre16.g692050.t1.1 | ER-Golgi Qa-SNARE protein, Syntaxin5/Syx5/Sed5/Syp3-family | |||
| Cre16.g676650.t1.1 | AP1G1 | Gamma1-Adaptin | ||
| Cre02.g099000.t1.1 | Late endosomal Qc-SNARE protein, Syx6/Tlg1/Syp5/6-family | |||
| Cre12.g554200.t1.2 | ER-Golgi Qb-SNARE, Memb/GS35/Bos1-family | |||
| Cre06.g310000.t1.1 | AP4E1 | Epsilon4-Adaptin | ||
| Cre10.g421250.t1.1 | EXO70 | Hypothetical Conserved Protein. Similar to Exo70, a subunit of the exocyst complex | ||
| Cre07.g330950.t1.1 | AP4S4 | Sigma4-Adaptin | ||
| Cre12.g488850.t1.2 | Adaptin, alpha/gamma/epsilon | |||
| division | Cre06.g269950.t1.1 | CDC48 | Protein involved in ubiquitin-dependent degradation of ER-bound substrates | |
| Cre08.g359200.t1.2 | Regulator of chromosome condensation (RCC1) | |||
| organisation | Cre13.g588600.t1.2 | Kinesin (SMY1 subfamily) | ||
| Cre12.g513450.t1.1 | TUH1 | Eta-Tubulin | ||
| Cre01.g010950.t1.2 | 26S proteasome regulatory complex, subunit PSMD10 (Ankyrin repeat) | |||
| Cre16.g679650.t1.2 | Fimbrin/Plastin | |||
| Cre06.g261950.t1.1 | Myotrophin and similar proteins (Ankyrin repeat) | |||
| Cre06.g291700.t1.1 | RSP3 | Radial spoke protein 3 | ||
| Cre10.g446700.t1.1 | ANK28 | Ankyrin repeat and DHHC-type Zn-finger domain containing proteins | ||
| Hormone metabolism† | abscisic acid | Cre16.g657800.t1.2 | CCD3 | Carotenoid cleavage dioxygenase |
| auxin | Cre14.g609900.t1.1 | Predicted membrane protein, contains DoH and Cytochrome b-561/ferric reductase transmembrane domains | ||
| brassinosteroid | Cre16.g663950.t1.1 | Sterol C5 desaturase | ||
| Cre02.g092350.t1.1 | Cytochrome P450, CYP51 superfamily; sterol 14 desaturase | |||
| Cre12.g557900.t1.1 | CDI1 | C-8,7 sterol isomerase | ||
| Cre02.g076800.t1.1 | Delta14-sterol reductase, mitochondrial | |||
| Cre12.g500500.t1.2 | 24-methylenesterol C-methyltransferase | |||
| ethylene | Cre02.g108450.t1.1 | FAP280 | Flagellar Associated Protein, transcriptional coactivator-like, putative transcription factor | |
| jasmonate | Cre19.g756100.t1.1 | NF* | ||
| Misc | acid and other phosphatases | Cre09.g396900.t1.1 | NADH pyrophosphatase I of the Nudix family of hydrolases | |
| Cre06.g259650.t1.1 | Calcineurin-like phosphoesterase, Acid-phosphatase-related | |||
| Cre06.g249800.t1.1 | Sphingomyelin synthetase -related | |||
| cytochrome P450 | Cre05.g234100.t1.1 | Cytochrome P450, CYP197 superfamily | ||
| dynamin | Cre02.g079550.t1.1 | DRP2 | Dynamin-related GTPase, involved in circadian rhythms | |
| Cre05.g245950.t1.1 | DRP1 | Dynamin-related GTPase | ||
| glutathione S transferases | Cre03.g154950.t1.1 | Glutathione S-transferase | ||
| misc2 | Cre12.g538450.t1.1 | EPT1 | CDP-Etn:DAG Ethanolamine phosphotransferase | |
| short chain dehydrogenase/reductase (SDR) | Cre12.g556750.t1.2 | Short-chain dehydrogenase/reductase | ||
| Cre08.g384864.t1.1 | SH3 domain, protein binding | |||
| Cre27.g775000.t1.1 | NF* | |||
| Cre17.g731350.t1.2 | Short chain dehydrogenase | |||
| UDP glucosyl and glucoronyl transferases | Cre02.g111150.t1.2 | ELG26 | Exostosin-like glycosyltransferase | |
| Cre02.g144050.t1.1 | Acetylglucosaminyltransferase EXT1/exostosin 1 | |||
| Cre03.g204050.t1.2 | ELG6 | Exostosin-like glycosyltransferases | ||
| Cre11.g474450.t1.1 | NF* | |||
| Cre03.g173300.t1.1 | Lactosylceramide 4-alpha-galactosyltransferase (alpha- 1,4-galactosyltransferase) | |||
| Cre02.g116600.t1.1 | ELG23 | Exostosin-like glycosyltransferase | ||
| Down-regulated genes | ||||
| Hormone metabolism† | cytokinin | Cre18.g744950.t1.2 | NF* | |
| Cre16.g678900.t1.1 | Response regulator receiver domain | |||
| Cre01.g040450.t1.1 | HDT1 | Histidine-aspartic acid phosphotransferase 1 (phosphorylation cascade) | ||
| ethylene | Cre09.g403550.t1.1 | Iron/ascorbate family oxidoreductases | ||
| Nucleotide metabolism | deoxynucleotide metabolism | Cre12.g491050.t1.1 | RIR2 | Ribonucleotide reductase (RNR), small subunit |
| Cre12.g492950.t1.1 | RIR1 | Ribonucleotide reductase (RNR), large subunit, class I | ||
| Cre16.g667850.t1.1 | dUTP pyrophosphatase | |||
| synthesis | Cre14.g614300.t1.1 | Inosine-5-monophosphate dehydrogenase/GMP reductase | ||
| Cre07.g318750.t1.1 | Phosphoribosylformylglycinamidine cyclo-ligase | |||
| Tetrapyrrole synthesis | porphobilinogen deaminase | Cre16.g663900.t1.1 | Porphobilinogen deaminase | |
| protochlorophyllide reductase | Cre01.g015350.t1.1 | Light-dependent protochlorophyllide reductase | ||
| urogen III methylase | Cre02.g133050.t1.2 | NF* | ||
| DNA | repair | Cre16.g670550.t1.2 | XP-G/RAD2 DNA repair endonuclease | |
| synthesis/chromatin structure | Cre07.g338000.t1.1 | MCM2 | Minichromosome maintenance protein | |
| Cre07.g314900.t1.2 | ATP-dependent RNA helicase, DEAD/DEAH helicase | |||
| Cre03.g172950.t1.1 | CBF5 | Centromere/microtubule binding protein | ||
| Cre01.g015250.t1.1 | Eukaryotic DNA polymerase delta | |||
| Cre27.g774200.t1.2 | NF* | |||
| Cre07.g316850.t1.1 | MCM4 | Minichromosome maintenance protein | ||
| unspecified | Cre10.g451250.t1.2 | Adenylate and guanylate cyclase catalytic domain, 3-5 exonuclease | ||
| Cre01.g059950.t1.2 | NF* | |||
*
Corresponding gene model was not found in v5.
†
Functional terms are inferred by homology to the annotation set of Arabidopsis thaliana (Lopez et al., 2011).