Table 1 List of the 50 genes that are most highly co-expressed with PSY

Phytoene synthase (PSY)

^{CMP, Pd, CPl}

Expressed protein (ExPr)

^{Pd, CPl}

Snowy cotyledon 1 (SCO1), Elongation factor Tu

^{CO, Pd, CPl, TF}

Transmembrane domain, oxidoreductase

^{Pd, PP, TP, CPl}

Uridylyltransferase-related

^{AB, TS, Cd, Pd, PP, TP, CPl}

Photosystem II reaction center PsbP family protein (PPL1)

^{PS, Pd, PP, TP, CPl}

Similar to LPA1 (Low PSII accum1),

^{Pd, PP, TP, CPl}

Chloroplast RNA binding (CRB)

^{AB, CO, TS, Cd, Cd, Pd, PP, CPl}

GCN5-related N-acetyltransferase (GNAT) family protein

Glyceraldehyde-3-phosphate dehydrogenase B subunit (GAPB)

^{PS, AB, TS, Cd, PM, PSD, Pd, PP, TP, CPl}

ExPr//chloroplast stroma

Thioredoxin X (ATHX)

^{Pd, CPl}

Rubredoxin family protein

^{PM, Pd, PP, TP, CPl}

Fu-gaeri1 (FUG1), Translation initiation factor IF-2, chloroplast

^TF

ExPr//chloroplast thylakoid membrane

^{Pd, PP, TP, CPl}

Phosphate transporter 2;1 (PHT2;1)

^{Pd, PP, CPl}

Glutamate synthase 1 (GLU1)/ferredoxin-dependent

^{AB, Pd, CPl, OR}

Preprotein translocase secA subunit, chloroplast [precursor]

Aminomethyltransferase, mitochondrial precursor

Photosystem I light harvesting complex gene 5 (LHCA5)

^{PS, PM, PSL, TP}

Ribulose bisphosphate carboxylase/oxygenase activase, putative

^{Pd, PP, TP, CPl}

Fructose-bisphosphate aldolase 1 (FBA1)

^{PM, Pd, PP, CPl, CF}

Encodes subunit NDH-N of NAD(P)H:plastoquinone dehydrogenase

^{Pd, PP, TP, CPl}

NAD(P)H dehydrogenase 18 (NDH18)

^{Pd, PP, TP, CPl}

NDH-dependent cyclic electron flow 1 (NDF1)

^{Pd, CPl}

ExPr

^{Pd, CPl}

Rubredoxin family protein, enhancer of sos3-1 (ENH1)

^{PM, Pd, PP, TP, CPl}

Ribose 5-phosphate isomerase-related

^{PS, PM, PSD, Pd, PP, TP, CPl, CF}

Membrane-associated zinc metalloprotease

^Pd

GTP-binding protein LepA, putative

^{Pd, CPl, TF}

High chlorophyll fluorescence 136 (HCF136) PS II assembly,

^{Pd, PP, TP, CPl}

Glycine cleavage system H protein, mitochondrial precursor

^OR

Tetratricopeptide repeat (TPR)-containing protein l

Membrane protein, putative contains 12 transmembrane domains

^{Pd, PP, CPl}

Thylakoid formation1 (THF1)

^{PS, PM, PSL, Pd, PP, TP, CPl}

Phytoene desaturation 2 (PDS2), UbiA prenyltransferase

ExPr

Fructose-1,6-bisphosphatase, putative

^{AB, TS, Cd, PM, Pd, PP, CF}

Lycopene cyclase (LCY-β)

^{CMP, Pd, CPl,}

Embryo sac development arrest 3 (EDA3), Heat shock protein 40

^{Pd, CPl}

Lecithin:cholesterol acyltransferase family protein (LACT)

Albino or pale green mutant (APGM), MPBQ methyltransferase

^{Pd, PP, CPl}

Calcineurin-like phosphoesterase family protein

^{Pd, CPl}

Oxygen-evolving complex-related

^{Pd, PP, TP, CPl}

PPR repeat-containing protein

Zetacarotene desaturase (ZDS)

^CMP

Thylakoid lumenal 29.8 kDa protein i

^{PS, Pd, PP, TP, CPl}

ExPr

DNAJ heat shock protein,

^{Pd, PP, TP, CPl}

Light-harvesting-like protein (Lil3:1)

^{Pd, PP, TP, CPl}

ExPr