Table 4. Analyses of transcripts involved in carotenoid biosynthesis, chlorophyll and ABA metabolism.

Gene ID	RPKM			Nr-annotation
	T1	T2	T3
Chlorophyll metabolism
Cs3g03100	69.88	63.55	72.16	Probable glutamate-tRNA ligase [Arabidopsis thaliana]
Cs8g01360	56.22	59.50	59.42	Glutamate-tRNA ligase 1 [Arabidopsis thaliana]
Cs3g16730	78.03	66.88	70.76	Glutamyl-tRNA reductase 1 [Arabidopsis thaliana]
Orange1.1t02623	89.64	138.40	164.18	Glutamate-1-semialdehyde 2,1-aminomutase 1, Chloroplastic [Arabidopsis thaliana]
Cs3g19770	35.03	42.97	62.68	Delta-aminolevulinic acid dehydratase, chloroplastic [Arabidopsis thaliana]
Cs7g13850	16.13	23.66	30.83	Porphobilinogen deaminase [Arabidopsis thaliana]
Cs5g12440	21.59	19.34	27.86	Uroporphyrinogen decarboxylase 1, chloroplastic
Cs7g30080	53.66	58.13	83.90	Uroporphyrinogen decarboxylase 2, chloroplastic
Orange1.1t02279	37.48	71.77	87.12	Coproporphyrinogen-III oxidase, chloroplastic
Cs5g06770	4.31	6.90	7.22	Oxygen-independent coproporphyrinogen-III oxidase 1
Cs2g24910	21.98	25.25	31.77	Protoporphyrinogen oxidase, chloroplastic/mitochondrial
Orange1.1t01782	35.37	56.42	53.75	Protoporphyrinogen oxidase, chloroplastic
Cs9g13460	44.52	5.36	17.65	Magnesium-chelatase subunit H
Cs2g30990	16.52	19.32	21.84	Magnesium-chelatase 67 kDa subunit
Cs2g05100	118.46	82.35	183.85	Magnesium-chelatase subunit ChlI-1, chloroplastic
Cs7g19710	6.74	3.42	18.65	Magnesium-protoporphyrin O-methyltransferase
Cs6g16200	76.55	14.23	116.31	Magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase 1
Cs1g06850	22.97	15.00	167.60	Protochlorophyllide reductase A, chloroplastic
Cs5g16830	5.28	29.95	0.81	Chlorophyllase type 0
Cs9g07520	30.05	13.07	20.43	Chlorophyllase type 0
Cs6g08720	57.16	45.38	61.05	Bacteriochlorophyll synthase 34 kDa chain
Cs3g19690	47.34	3.63	10.36	Chlorophyll synthase, putative [Ricinus communis]
Cs4g15890	56.44	69.89	61.91	Chlorophyll (ide) b reductase NOL, chloroplastic
Cs7g24010	5.24	11.18	13.54	Chlorophyll (ide) b reductase NOL, chloroplastic
Cs8g15480	64.04	92.78	73.45	Pheophorbide a oxygenase, chloroplastic
Cs1g22670	37.78	73.56	82.11	Red chlorophyll catabolite reductase, chloroplastic
Carotenoid biosynthesis
Cs6g15910	79.73	216.13	172.64	Phytoene synthase
Orange1.1t02108	30.15	85.62	32.83	PREDICTED: phytoene synthase 2, chloroplastic-like [Vitis vinifera]
Orange1.1t02361	50.61	63.09	64.41	Phytoene dehydrogenase, chloroplastic/chromoplastic
Cs5g24730	47.11	59.11	58.21	15-cis-zeta-carotene isomerase, chloroplastic
Cs3g11180	56.36	81.36	70.96	Phytoene dehydrogenase, chloroplastic/chromoplastic
Cs6g13340	25.39	26.28	23.76	Prolycopene isomerase 1, chloroplastic
Cs4g14850	7.43	5.56	10.07	Capsanthin/capsorubin synthase, chromoplast
Orange1.1t00772	9.33	8.65	11.12	Capsanthin/capsorubin synthase, chromoplast
Orange1.1t01058	38.85	39.93	39.95	Cytochrome P450 97B1, chloroplastic
Cs9g19270	1038.75	1722.54	1359.83	Beta-carotene 3-hydroxylase 1, chloroplastic
Cs1g22620	65.41	82.35	95.98	3-hydroxybenzoate 6-hydroxylase 1
Orange1.1t04051	1.01	0.95	1.10	3-hydroxybenzoate 6-hydroxylase 1
Cs5g26080	11.76	9.88	16.31	Violaxanthin de-epoxidase, chloroplastic
Orange_new Gene_1755	0.45	3.82	9.60	Lycopene beta-cyclase [Citrus×paradisi]
ABA metabolism
Cs8g13780	4.47	3.20	4.51	Indole-3-acetaldehyde oxidase
Cs6g01180	46.39	38.09	60.42	Xanthoxin dehydrogenase
Cs2g03270	2.08	67.84	18.90	9-cis-epoxycarotenoid dioxygenase 2 [Citrus sinensis]
Cs5g14370	28.65	20.09	8.45	Putative 9-cis-epoxycarotenoid dioxygenase 3 [Citrus sinensis]
Cs7g14820	2.18	0.26	5.90	Carotenoid cleavage dioxygenase 4a [Citrus clementina]
Cs9g11260	0.00	0.00	0.00	Carotenoid 9,10(9,10′)-cleavage dioxygenase 1
Cs6g19380	60.57	30.48	9.86	ABA 8' -hydroxylase [Citrus sinensis]
Cs8g05940	2.05	3.80	3.20	Abscisic acid 8′-hydroxylase 1
Cs8g18780	1.10	0.78	0.27	ABA 8' -hydroxylase [Citrus sinensis]