Table S3.
Genes differentially expressed in H82 cells with an FDR < 0.05, compared with those in WT and C-1 cells in LC conditions for 2 h
| Gene ID* | Gene name | Average FPKM in WT | Average FPKM in H82 | Average FPKM in C-1 | Description of gene product | q value (WT LC 2 h vs. H82 LC 2 h) | q value (C-1 LC 2 h vs. H82 LC 2 h) | q value (WT LC 2 h vs. C-1 LC 2 h) | WT LC 2 h FPKM/H82 LC 2 h FPKM | C-1 LC 2 h FPKM/H82 LC 2 h FPKM | ||||||
| HC | LC 0.3 h | LC 2 h | HC | LC 0.3 h | LC 2 h | HC | LC 0.3 h | LC 2 h | ||||||||
| Cre02.g097800 | HLA3 | 2.1 | 55.0 | 152.3 | 2.5 | 22.4 | 7.0 | 1.9 | 35.4 | 154.3 | Plasma membrane-localized ATP-binding cassette transporter associated with HCO3– uptake | 2.14.E−03 | 2.14.E−03 | 9.98.E−01 | 21.8 | 22.1 |
| Cre12.g497300 | CAS | 367.7 | 152.1 | 264.9 | 6.0 | 6.1 | 7.1 | 99.4 | 95.2 | 89.2 | Thylakoid membrane-localized calcium-binding protein containing Rhodanese-like domain | 2.14.E−03 | 2.14.E−03 | 3.92.E−02 | 37.4 | 12.6 |
| Cre03.g204577 | DNJ31 | 3.0 | 4.0 | 13.2 | 2.6 | 2.9 | 2.9 | 3.0 | 3.3 | 26.6 | DnaJ-like chaperonin | 2.14.E−03 | 2.14.E−03 | 2.13.E−01 | 4.6 | 9.3 |
| Cre05.g248400 | CAH4 | 7.4 | 756.1 | 2,335.8 | 3.0 | 499.4 | 296.1 | 6.4 | 712.7 | 2,329.5 | Mitochondrial carbonic anhydrase, CA4 | 2.14.E−03 | 2.14.E−03 | 9.98.E−01 | 7.9 | 7.9 |
| Cre05.g248450 | CAH5 | 8.5 | 749.9 | 2,134.9 | 3.4 | 485.7 | 289.7 | 6.4 | 694.1 | 2,243.7 | Mitochondrial carbonic anhydrase, CA5 | 2.14.E−03 | 2.14.E−03 | 9.98.E−01 | 7.4 | 7.7 |
| Cre07.g334750 | PPP30 | 2.4 | 16.4 | 15.2 | 2.2 | 16.0 | 3.2 | 1.6 | 33.0 | 20.2 | Type 2C protein phosphatase containing Stage II sporulation protein E (SpoIIE) (PF07228) domain | 5.41.E−03 | 2.14.E−03 | 8.71.E−01 | 4.8 | 6.4 |
| Cre06.g309000 | LCIA | 2.5 | 626.8 | 798.5 | 2.1 | 533.6 | 151.1 | 0.6 | 911.0 | 866.5 | Chloroplast envelope-localized possible anion channel associated with inorganic carbon uptake; nitrite transporter (NAR1) homolog | 2.14.E−03 | 2.14.E−03 | 9.98.E−01 | 5.3 | 5.7 |
| Cre04.g223300 | CCP1 | 3.1 | 466.2 | 632.6 | 2.4 | 308.7 | 137.7 | 0.7 | 428.7 | 700.0 | Low-CO2–inducible chloroplast envelope protein (LIP36-1) | 2.14.E−03 | 2.14.E−03 | 9.97.E−01 | 4.6 | 5.1 |
| Cre12.g541550 | — | 7.7 | 6.7 | 24.3 | 33.6 | 15.5 | 6.8 | 48.3 | 27.0 | 34.4 | † | 2.14.E−03 | 2.14.E−03 | 4.55.E−01 | 3.6 | 5.1 |
| Cre26.g756747 | — | 1.3 | 157.5 | 41.0 | 1.0 | 137.8 | 13.6 | 0.4 | 279.4 | 67.1 | † | 2.14.E−03 | 2.14.E−03 | 2.34.E−01 | 3.0 | 4.9 |
| Cre04.g222800 | LCID | 10.5 | 39.3 | 61.9 | 5.8 | 30.0 | 17.6 | 4.2 | 59.2 | 82.2 | Homolog of low-CO2–inducible protein B (LCIB) | 2.14.E−03 | 2.14.E−03 | 6.97.E−01 | 3.5 | 4.7 |
| Cre08.g367400 | LHCSR3.2 | 1.6 | 245.1 | 164.3 | 2.0 | 236.3 | 46.0 | 1.7 | 340.6 | 208.8 | Stress-related chlorophyll a/b binding protein 3 | 2.14.E−03 | 2.14.E−03 | 8.02.E−01 | 3.6 | 4.5 |
| Cre08.g367500 | LHCSR3.1 | 1.6 | 290.1 | 191.8 | 1.9 | 263.9 | 49.7 | 2.9 | 341.6 | 223.2 | Stress-related chlorophyll a/b binding protein 3 | 2.14.E−03 | 2.14.E−03 | 9.39.E−01 | 3.9 | 4.5 |
| Cre04.g222750 | CCP2 | 5.5 | 150.4 | 199.3 | 3.4 | 151.7 | 69.9 | 3.4 | 234.5 | 280.6 | Low-CO2–inducible chloroplast envelope protein (LIP36-2) | 2.14.E−03 | 2.14.E−03 | 6.49.E−01 | 2.9 | 4.0 |
| Cre06.g281600 | LCI23 | 4.2 | 36.0 | 86.3 | 5.4 | 53.2 | 28.6 | 6.6 | 69.8 | 104.8 | Low-CO2–inducible septin-like protein | 2.14.E−03 | 2.14.E−03 | 8.91.E−01 | 3.0 | 3.7 |
| Cre02.g088551 | — | 5.2 | 14.0 | 22.2 | 4.1 | 12.5 | 8.9 | 5.9 | 22.3 | 32.1 | † | 2.14.E−03 | 2.14.E−03 | 4.27.E−01 | 2.5 | 3.6 |
| Cre11.g467617 | LCI19 | 4.2 | 15.2 | 28.0 | 3.8 | 16.2 | 8.8 | 3.5 | 19.3 | 29.5 | Low-CO2–inducible gamma hydroxybutyrate dehydrogenase | 2.14.E−03 | 2.14.E−03 | 9.98.E−01 | 3.2 | 3.4 |
| Cre09.g399400 | TGL15 | 11.6 | 8.7 | 15.2 | 1.4 | 2.9 | 3.6 | 1.9 | 4.9 | 12.0 | Triacylglycerol lipase | 2.14.E−03 | 2.14.E−03 | 7.20.E−01 | 4.2 | 3.3 |
| Cre05.g234652 | — | 17.7 | 29.3 | 50.5 | 13.5 | 32.5 | 17.4 | 17.3 | 47.6 | 55.9 | Predicted protein with CobW domain | 2.14.E−03 | 2.14.E−03 | 9.76.E−01 | 2.9 | 3.2 |
| Cre10.g439700 | CGL28 | 6.5 | 56.5 | 58.4 | 6.4 | 64.5 | 25.7 | 4.8 | 122.9 | 82.2 | RNA binding protein | 3.88.E−03 | 2.14.E−03 | 5.99.E−01 | 2.3 | 3.2 |
| Cre09.g391726 | — | 5.5 | 17.0 | 16.2 | 14.8 | 48.1 | 30.6 | 62.0 | 116.0 | 96.9 | † | 2.86.E−02 | 2.14.E−03 | 2.14.E−03 | 0.5 | 3.2 |
| Cre17.g720950 | SRD3 | 14.4 | 89.7 | 28.2 | 11.4 | 91.5 | 14.1 | 17.2 | 223.0 | 43.5 | Putative 3-oxo-5-alpha-steroid 4-dehydrogenase | 1.29.E−02 | 2.14.E−03 | 2.81.E−01 | 2.0 | 3.1 |
| Cre02.g080800 | — | 2.8 | 8.2 | 10.6 | 2.7 | 9.7 | 4.6 | 2.1 | 14.8 | 14.1 | † | 2.14.E−03 | 2.14.E−03 | 6.04.E−01 | 2.3 | 3.1 |
| Cre03.g162800 | LCI1 | 2.6 | 2,144.6 | 2,496.1 | 2.3 | 1,403.0 | 927.0 | 1.5 | 1,833.1 | 2,674.8 | Plasma membrane-localized protein associated with inorganic carbon transport | 2.18.E−02 | 1.61.E−02 | 9.98.E−01 | 2.7 | 2.9 |
| Cre03.g168100 | — | 7.4 | 18.5 | 32.9 | 6.6 | 17.1 | 17.0 | 8.9 | 33.0 | 46.9 | † | 3.02.E−02 | 2.14.E−03 | 4.75.E−01 | 1.9 | 2.8 |
| Cre03.g151650 | SMM7 | 2.5 | 24.2 | 16.1 | 1.8 | 27.3 | 5.1 | 1.8 | 35.4 | 13.4 | Lysine methyltransferase | 2.14.E−03 | 2.14.E−03 | 8.26.E−01 | 3.2 | 2.6 |
| Cre10.g463370 | — | 6.8 | 2.5 | 3.8 | 2.7 | 1.8 | 1.3 | 3.3 | 2.4 | 3.2 | Putative smooth-muscle-myosin-light-chain kinase | 8.15.E−03 | 2.79.E−02 | 9.30.E−01 | 3.0 | 2.6 |
| Cre02.g077750 | FAP211 | 2.7 | 3.1 | 4.1 | 4.5 | 5.1 | 9.0 | 5.8 | 13.0 | 22.9 | Flagellar-associated protein | 2.14.E−03 | 2.14.E−03 | 2.14.E−03 | 0.5 | 2.5 |
| Cre03.g183300 | — | 19.8 | 46.3 | 18.6 | 10.5 | 42.9 | 7.9 | 14.5 | 59.3 | 19.3 | Predicted protein with starch-binding domain | 2.45.E−02 | 2.36.E−02 | 9.98.E−01 | 2.4 | 2.5 |
| Cre03.g189350 | — | 80.3 | 69.2 | 129.6 | 50.2 | 54.1 | 47.2 | 53.3 | 79.7 | 112.0 | † | 2.14.E−03 | 2.14.E−03 | 9.12.E−01 | 2.8 | 2.4 |
| Cre06.g295450 | HPR1 | 65.8 | 158.6 | 144.4 | 39.6 | 211.7 | 71.8 | 61.7 | 283.8 | 166.2 | Hydroxypyruvate reductase | 3.49.E−02 | 1.50.E−02 | 9.49.E−01 | 2.0 | 2.3 |
| Cre05.g241950 | ASC2 | 217.0 | 191.7 | 374.2 | 174.9 | 184.6 | 152.9 | 239.0 | 287.3 | 351.3 | Voltage-dependent anion-selective channel | 6.84.E−03 | 2.45.E−02 | 9.98.E−01 | 2.5 | 2.3 |
| Cre09.g398500 | — | 60.6 | 35.3 | 66.2 | 10.7 | 16.8 | 22.7 | 14.7 | 28.8 | 51.7 | † | 2.14.E−03 | 5.41.E−03 | 7.53.E−01 | 2.9 | 2.3 |
| Cre09.g404750 | SRR2 | 8.7 | 6.3 | 11.5 | 3.3 | 3.9 | 5.6 | 2.7 | 5.5 | 12.1 | Scavenger receptor cysteine-rich (SRCR) protein | 6.84.E−03 | 2.14.E−03 | 9.98.E−01 | 2.1 | 2.2 |
| Cre06.g281450 | SRR22 | 12.3 | 8.6 | 12.6 | 3.3 | 3.9 | 5.5 | 3.2 | 5.4 | 11.5 | Scavenger receptor cysteine-rich (SRCR) protein | 2.14.E−03 | 9.41.E−03 | 9.71.E−01 | 2.3 | 2.1 |
| Cre14.g621650 | MCT1 | 72.9 | 93.2 | 101.6 | 48.0 | 87.5 | 48.0 | 56.7 | 99.6 | 98.9 | Acyl-carrier-protein, S-malonyltransferase | 1.80.E−02 | 3.02.E−02 | 9.98.E−01 | 2.1 | 2.1 |
| Cre07.g343050 | — | 7.7 | 16.6 | 26.0 | 7.9 | 16.0 | 13.7 | 6.5 | 14.8 | 28.0 | † | 2.94.E−02 | 1.18.E−02 | 9.93.E−01 | 1.9 | 2.1 |
| Cre12.g531900 | — | 33.4 | 41.0 | 48.6 | 16.6 | 36.7 | 22.8 | 26.7 | 47.8 | 45.3 | † | 1.80.E−02 | 3.11.E−02 | 9.98.E−01 | 2.1 | 2.0 |
| Cre09.g398250 | — | 60.3 | 33.2 | 42.2 | 10.6 | 17.3 | 19.9 | 15.8 | 30.3 | 39.1 | † | 1.61.E−02 | 2.79.E−02 | 9.95.E−01 | 2.1 | 2.0 |
| Cre01.g030350 | CGL41 | 2.2 | 3.5 | 3.5 | 3.4 | 6.5 | 8.9 | 4.0 | 4.0 | 17.4 | Predicted RbcX protein | 2.14.E−03 | 3.71.E−02 | 2.14.E−03 | 0.4 | 2.0 |
| Cre17.g710300 | — | 18.3 | 10.0 | 4.6 | 20.8 | 23.3 | 11.6 | 19.9 | 21.1 | 22.6 | Pherophorin (DUF3707) | 2.14.E−03 | 3.84.E−02 | 2.14.E−03 | 0.4 | 2.0 |
| Cre13.g573250 | — | 30.8 | 32.1 | 25.8 | 13.0 | 25.4 | 13.3 | 17.6 | 41.6 | 24.5 | Thiosulfate sulfurtransferase with Rhodanese-like domain | 1.80.E−02 | 4.84.E−02 | 9.98.E−01 | 1.9 | 1.8 |
| Cre02.g093750 | NRX2 | 11.2 | 9.8 | 7.6 | 8.7 | 18.9 | 17.1 | 7.4 | 14.2 | 8.9 | Nucleoredoxin 2 | 2.14.E−03 | 2.45.E−02 | 8.99.E−01 | 0.4 | 0.5 |
| Cre12.g546550 | FEA1 | 277.5 | 36.5 | 4.7 | 136.0 | 26.5 | 17.2 | 172.6 | 65.9 | 6.4 | Fe-assimilating protein; High-CO2 inducible protein H43 | 2.14.E−03 | 9.41.E−03 | 6.27.E−01 | 0.3 | 0.4 |
| Cre05.g244400 | — | 1.6 | 2.4 | 2.1 | 3.1 | 6.7 | 6.2 | 2.1 | 3.4 | 1.9 | Nucleotide-diphospho-sugar transferase | 2.94.E−02 | 2.94.E−02 | 9.97.E−01 | 0.4 | 0.3 |
*
Gene ID, phytozome gene accession number.
†
Gene product that is not annotated.