Table 1.

RNA‐Seq analysis on nucleus genes encoding subunits of photosystem I (PSI) and photosystem II (PSII) and encoding steps of the chlorophyll biosynthetic pathway

AGI no.	Gene ID	Function	1 day				7 days
			WT	sig2‐2	sig2‐2 /WTa	Cutoffb	WT	sig2‐2	sig2‐2 /WTa	Cutoffb
At3g61470	LHCA2	PSI	18	37	1.0	Yes	2,241	1,869	−0.3	No
At1g61520*	LHCA3	PSI	39	84	1.1	Yes	3,841	3,633	−0.1	No
At1g29920	LHCB1.1	PSII	8	20	1.4	Yes	4,303	5,953	0.5	Yes
At1g29930	LHCB1.3	PSII	128	281	1.1	Yes	16,930	35,208	1.1	No
At2g34430	LHCB1.4	PSII	1	2	0.8	No	1,637	3,190	1.0	Yes
At2g34420	LHCB1.5	PSII	24	56	1.2	Yes	3,759	5,292	0.5	Yes
At3g27690*	LHCB2.4	PSII	1	1	−0.9	No	766	342	−1.2	Yes
At5g54270	LHCB3	PSII	35	73	1.1	Yes	2,773	2,570	−0.1	No
At5g01530*	LHCB4.1	PSII	59	119	1.0	Yes	2,643	2,319	−0.2	No
At2g40100*	LHCB4.3	PSII	4	7	0.6	No	26	5	−2.4	Yes
At4g10340*	LHCB5	PSII	48	93	1.0	Yes	3,510	2,915	−0.3	No
At2g20260*	PsaE	PSI	16	40	1.3	Yes	750	717	−0.1	No
At3g16140*	PsaH1	PSI	15	31	1.1	Yes	1,306	1,177	−0.1	No
At1g30380*	PsaK	PSI	11	37	1.8	Yes	2,799	2,050	−0.4	Yes
At4g12800*	PsaL	PSI	23	57	1.3	Yes	2,857	1,978	−0.5	Yes
At1g08380*	PsaO	PSI	14	28	1.0	Yes	3,624	2,607	−0.5	Yes
At4g05180*	PsbQ‐2	PSII	2	6	1.5	Yes	1,308	812	−0.7	Yes
At1g79040*	PsbR	PSII	59	126	1.1	Yes	5,064	4,319	−0.2	No
At5g54190*	PORA	CP	8	17	1.1	Yes	12	5	−1.2	Yes
At1g03630*	PORC	CP	69	80	0.2	No	196	82	−1.3	Yes

Genes were selected by >2‐fold change with significant cutoff (yes or no) in at least one sample between 1 and 7 days from RNA‐Seq analysis. Photosystem I (PSI) and PSII‐related genes, nuclear‐encoded; chlorophyll biosynthetic pathway genes (CP), nuclear‐encoded.

^aFold change (in log2 scale).

^bSignificant with q‐value <.05. Asterisks on AGI no. indicates genes, downregulated by retrograde signals as identified by microarray analysis from Tables S6–S7 of Woodson et al. (2013).