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. Author manuscript; available in PMC: 2019 Sep 18.
Published in final edited form as: Nat Genet. 2019 Mar 18;51(4):627–635. doi: 10.1038/s41588-019-0370-6

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
a

Prediction of protein localization by PredAlgo56: C = chloroplast, M = mitochondrion, SP = secretory pathway, O = other.

b

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.

c

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.

d

the FDR for that gene compared to all alleles for all genes (see Supplementary Note).

e

Arabidopsis homolog, obtained from the “best_arabidopsis_TAIR10_hit_name” field in Phytozome12.

f

AT3G17040.1 is required for functional PSII in Arabidopsis whereas Cre09.g389615 was shown to be involved in PSI accumulation in Chlamydomonas.