Table 1 ∣.
Higher-confidence genes from the photosynthesis screen that had a previously known role in photosynthesis.
| Category | Gene | Defline/ description in Phytozome12 |
Pred Algoa |
Alleles in two replicates |
At homologe | Reference and the corresponding organism(s) |
||
|---|---|---|---|---|---|---|---|---|
| +b | −c | FDRd | ||||||
| Calvin-Benson-Bassham cycle | Cre03.g185550 (SEBP1, SBP1) | Sedoheptulose-1,7-bisphosphatase | C | 3 | 0 | 0.021 | AT3G55800.1 (SBPASE) | Arabidopsis29 |
| 3 | 0 | 0.018 | ||||||
| Cre12.g524500 (RMT2) | Rubisco small subunit N-methyltransferase | O | 3 | 0 | 0.021 | AT3G07670.1 | Pisum30 | |
| 3 | 0 | 0.018 | ||||||
| Cre06.g298300 (MRL1, PPR2) | Pentatricopeptide repeat protein, stabilizes rbcL mRNA | C | 1 | 1 | 1.000 | AT4G34830.1 (MRL1) | Chlamydomonas and Arabidopsis31 | |
| 2 | 0 | 0.239 | ||||||
| Carbon concentrating mechanism | Cre12.g497300 (CAS1, TEF2) | Rhodanese-like Ca-sensing receptor | C | 2 | 0 | 0.260 | AT5G23060.1 (CaS) | Chlamydomonas32 |
| 2 | 0 | 0.239 | ||||||
| Cre10.g452800 (LCIB) | Low-CO2-inducible protein | C | 2 | 0 | 0.260 | - | Chlamydomonas33 | |
| 1 | 1 | 1.000 | ||||||
| Chloroplast and thylakoid morphogenesis | Cre14.g616600 | - | M | 4 | 3 | 0.021 | AT1G03160.1 (FZL) | Arabidopsis34 |
| 4 | 3 | 0.018 | ||||||
| Cofactor and signaling molecule metabolism | Cre13.g581850 | - | M | 5 | 5 | 0.010 | AT4G31390.1 | Arabidopsis35 |
| 2 | 8 | 1.000 | ||||||
| Cre10.g423500 (HMOX1, HMO1) | Heme oxygenase | C | 3 | 0 | 0.021 | AT1G69720.1 (HO3) | Chlamydomonas14 | |
| 3 | 0 | 0.018 | ||||||
| Cre03.g188700 (PLAP6, PLP6) | Plastid lipid associated protein, Fibrillin | C | 3 | 1 | 0.070 | AT5G09820.2 | Arabidopsis36 | |
| 3 | 1 | 0.056 | ||||||
| Cre16.g659050 | - | C | 4 | 6 | 0.098 | AT1G68890.1 | Chlamydomonas37 | |
| 4 | 6 | 0.075 | ||||||
| PSI protein synthesis and assembly | Cre12.g524300 (CGL71) | Predicted protein | C | 2 | 0 | 0.260 | AT1G22700.1 | Synechocystis38; Arabidopsis39; Chlamydomonas40 |
| 2 | 0 | 0.239 | ||||||
| Cre01.g045902 | - | C | 1 | 1 | 1.000 | AT3G24430.1 (HCF101) | Arabidopsis41,42 | |
| 2 | 0 | 0.239 | ||||||
| PSI RNA splicing and stabilization | Cre09.g389615 | - | M | 5 | 0 | 0.0002 | AT3G17040.1 (HCF107) | Chlamydomonas43; Arabidopsis42,44,f |
| 5 | 0 | 0.0002 | ||||||
| Cre01.g027150 (CPLD46, HEL5) | DEAD/DEAH-box helicase | M | 5 | 1 | 0.0004 | AT1G70070.1 (EMB25, ISE2, PDE317) | Arabidopsis45 | |
| 5 | 1 | 0.0003 | ||||||
| Cre09.g394150 (RAA1) | - | M | 5 | 1 | 0.0004 | - | Chlamydomonas46 | |
| 5 | 1 | 0.0003 | ||||||
| Cre12.g531050 (RAA3) | PsaA mRNA maturation factor 3 | C | 3 | 0 | 0.021 | - | Chlamydomonas47 | |
| 3 | 0 | 0.018 | ||||||
| Cre10.g440000 (OPR120) | - | C | 2 | 0 | 0.260 | - | Chlamydomonas48,49 | |
| 2 | 0 | 0.239 | ||||||
| PSII protein synthesis and assembly | Cre13.g578650 (CPLD10, NUOAF5) | Similar to complex I intermediate-associated protein 30 | C | 3 | 3 | 0.260 | AT1G16720.1 (HCF173) | Arabidopsis42,50,51 |
| 3 | 3 | 0.208 | ||||||
| Cre02.g073850 (CGL54) | Predicted protein | C | 2 | 0 | 0.260 | AT1G05385.1 (LPA19, Psb27-H1) | Arabidopsis52 | |
| 2 | 0 | 0.239 | ||||||
| Cre02.g105650 | - | C | 2 | 0 | 0.260 | AT5G51545.1 (LPA2) | Arabidopsis53 | |
| 2 | 0 | 0.239 | ||||||
| Cre06.g273700 (HCF136) | - | C | 2 | 0 | 0.260 | AT5G23120.1 (HCF136) | Arabidopsis42; Synechocystis54 | |
| 1 | 1 | 1.000 | ||||||
| Cre10.g430150 (LPA1, REP27) | - | C | 2 | 0 | 0.260 | AT1G02910.1 (LPA1) | Arabidopsis55 | |
| 1 | 1 | 1.000 | ||||||
Prediction of protein localization by PredAlgo56: C = chloroplast, M = mitochondrion, SP = secretory pathway, O = other.
The number of exon/intron/5’UTR mutant alleles for that gene that satisfy our requirement of minimum 50 reads and showed at least 10X fewer normalized reads in the TP-light sample compared to the TAP-dark sample.
The number exon/intron/5’UTR mutant alleles for that gene that satisfy our minimum read count requirement but did not satisfy the at least 10X depletion in TP-light criterion.
the FDR for that gene compared to all alleles for all genes (see Supplementary Note).
Arabidopsis homolog, obtained from the “best_arabidopsis_TAIR10_hit_name” field in Phytozome12.
AT3G17040.1 is required for functional PSII in Arabidopsis whereas Cre09.g389615 was shown to be involved in PSI accumulation in Chlamydomonas.