supporting files for "Cytokinin down-regulates photosystem II photochemistry during prolonged darkness in a phytochrome B-dependent manner"

 Fig.1_source data. Source data for panel A of Fig.1: chlorophyll a+b content and chlorophyl a/b ratio in Arabidopsis Col-0 rosette leaves of 33-days old plants that were detached and treated with mock (0.2% DMSO), BAP or MTU at the concentration of 0.5 or 5 µM, and kept for 2, 5, 7, 9 or 12 days in the dark (days after detachment and darkening, dad).

 Fig.2_source data. Source data for each panel of Fig.2: (A) Maximum quantum yield of PSII photochemistry (F_V/F_M). (B) Quantum yields of PSII photochemistry (Φ_P), regulatory non-photochemical quenching (Φ_NPQ), and non-regulatory dissipation processes (Φ_f,D). (C) Electron transport rates through PSII (ETRII), PSI (ETRI), and cyclic electron transport (CET). (D) ROS accumulation visualized using 2′,7′-dichlorodihydrofluorescein diacetate (DCF-DA) and quantified from mean green-fluorescence intensity. (E) F_V/F_M in cytokinin receptor double mutants and selected cytokinin response-regulator mutants. Detached leaves were incubated with mock (0.2% DMSO) or 5 µM BAP in darkness for 2 days. (F) F_V/F_M in cytokinin receptor double mutants and selected cytokinin response-regulator mutants. Detached leaves were incubated with mock (0.2% DMSO) or 5 µM MTU in darkness for 2 days.

Fig. 6_source data. Source data for Fig. 6: RT-qPCR analysis of ARR5, APX1, CAB1, HY5, and CCA1 transcript levels in detached leaves of 6-week-old Arabidopsis Col-0 and phyB mutant line treated with mock (0.2% DMSO), 5 µM BAP, or 5 µM MTU and kept in darkness for 2 days (2 DAD).

 Fig. 7_source data. Source data for each panel of Fig.7: (A) Maximum quantum yield of PSII photochemistry (F_V/F_M), (B) cyclic electron transport (CET), and (C) malondialdehyde (MDA) content, in detached leaves of WT, phytochrome-deficient mutants (phyA or phyB), and phytochrome B overexpressing line (phyB OE).

 Fig. 8_source data. Source data for panel A: Maximum quantum yield of PSII photochemistry (F_V/F_M) in hydroponically grown Arabidopsis WT or phyB mutant plants after 1 or 3 days in the dark. Plants were treated with mock (0.02 % DMSO), BAP or MTU at the concentration of 5 or 10 µM.

 Fig. S1_source data. Source data for Fig. S1: Maximum quantum yield of PSII photochemistry (F_V/F_M) in selected time points. Leaves from 33-day-old Arabidopsis WT plants (Col-0) were detached and incubated in the dark while submerged in solutions of 0.2% DMSO, 5 μM BAP, or 5 μM MTU for 2 days, and afterwards the F_V/F_M was measured (time point 1). The leaves were subsequently re-illuminated by returning them to the standard growing conditions (8-h light (110 µmol photons m-2 s-1; LED)/16-h dark cycle, and at 22/20 °C), and before the end of the photoperiod, F_V/F_M was measured again (time point 2). On the following day, approximately 3 h after the start of the photoperiod, the F_V/F_M was measured for the last time (time point 3).

 Fig. S4_source data. Source data for each panel of Fig. S3: (A) Root length and (B) number of lateral roots in Arabidopsis seedlings grown on 1/2 MS medium supplemented with mock (0.2% DMSO), BAP, or MTU at concentrations of 0.1, 1, 5, or 10 µM. (C) Representative images from the root inhibition assay. (D, E) Response of the TCSv2:3XVENUS reporter in Arabidopsis seedlings treated for 15 h with mock (0.2% DMSO), 10 µM BAP, or 10 µM MTU. (F) qPCR analysis of CK signaling-related genes in Arabidopsis Col-0 seedlings 1, 3, and 6 h after treatment with mock, 1 µM BAP, or 1 µM MTU.

Fig. S6_source data. Source data for Fig. S6: RT-qPCR analysis of ndhM, ndhN, WRKY6, CRR1, PHYA, and PHYB transcript levels in detached leaves of 6-week-old Arabidopsis Col-0 plants treated with mock (0.2% DMSO), 5 µM BAP, or 5 µM MTU and kept in darkness for 2 days (2 DAD).

Fig.S1-S8, Table_S1:

Fig. S1 Reversibility of F_V/F_M decrease upon re-illumination.

Fig. S2 PCA analysis of RNA-seq data.

Fig. S3 GO enrichment network of pathways responding to BAP/MTU treatments.

Fig. S4 Cytokinin root inhibition assay and signaling in response to BAP/MTU treatments.

Fig. S5 Proteomic analysis of BAP-treated leaves of Arabidopsis thaliana.

Fig. S6 RT-qPCR analysis in Arabidopsis thaliana wild-type leaves.

Fig. S7 Cytokinin-dependent transcriptional changes in light-signaling pathways.

Fig. S8 Spectrum of far-red light used in the study.

Table S1 List of RT-qPCR primers.

Table_S2 List of common genes that were responding under all experimental conditions.

Table_S3 GO enrichment analysis of genes responding to CK treatments (6, 48 h).

Table_S4 GO enrichment analysis of genes responding to CK treatments (30 min).

Table_S5 Differential protein analyses: All proteins responding to BAP and MTU treatments.

Table_S6 Classification of proteins responding to MTU treatment.

Table S7_Classification of proteins responding to BAP treatment.

Table S8_GO enrichment analysis of proteins responding to CK treatments.