Identification of differentially expressed photosynthesis- and sugar synthesis-related genes in tomato (Solanum lycopersicum) plants grown under different CO₂ concentrations

Figures & data

Table 1. Quality assessment of the sequencing results of each library.

Sample	Total reads	GC content	Mapped reads	Unique mapped reads	Multiple map reads
FQD1	51,641,154	43.33%	44,995,910 (87.13%)	44,592,631 (86.35%)	403,279 (0.78%)
FQD2	58,117,778	43.36%	50,767,970 (87.35%)	50,308,886 (86.56%)	459,084 (0.79%)
FQF1	40,931,460	43.29%	35,522,466 (86.79%)	35,210,892 (86.02%)	311,574 (0.76%)
FQF2	41,590,498	42.94%	36,286,677 (87.25%)	35,980,379 (86.51%)	306,298 (0.74%)

Table 2. Screening of differentially expressed genes (DEGs).

DEG fold change		FQD vs. FQF
>2	Total	208
	Up	179
	Down	29
2–10	Total	177
	Up	153
	Down	24
10–50	Total	29
	Up	25
	Down	4
>50	Total	2
	Up	1
	Down	1

Figure 1. Gene ontology (GO) analysis of differentially expressed genes (DEGs) from tomato. A total of 130 DEGs were categorized into 242 function items.

Figure 2. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of differentially expressed genes (DEGs) from tomato. A total of 21 signalling pathways were identified.

Table 3. Identification of key genes related to photosynthesis and sugar synthesis.

		Log2FC	GO annotation
Photosynthesis	Solyc01g007290.1	1.56	Photosynthesis, light reaction chloroplast thylakoid membrane
	Solyc01g007310.2	1.10	NADH dehydrogenase (ubiquinone) activity photosynthesis, light reaction electron transport chain
	Solyc01g007350.2	2.24	Photosystem I
	Solyc01g007520.2	2.31	Photosystem II photosynthesis phosphate ion binding
	Solyc01g007530.2	1.46	Respiratory electron transport chain electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity
	Solyc01g007540.2	1.88	Photosynthetic electron transport chain electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity
	Solyc01g017310.1	4.19	Photosystem I; photosynthesis electron transport chain
	Solyc01g048590.1	3.33	Photosynthetic electron transport in photosystem II
	Solyc02g011800.1	1.97	Oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor photosynthesis, light reaction
	Solyc06g009950.1	4.46	Electron carrier activity photosystem I
	Solyc07g032450.1	3.46	Photosynthesis electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity
	Solyc08g061900.1	2.92	NADH dehydrogenase (ubiquinone) activity ATP synthesis coupled electron transport
	Solyc09g015290.1	3.47	Electron carrier activity photosystem I photosynthesis
	Solyc09g055950.1	2.63	Photosynthetic electron transport in photosystem II electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity
	Solyc10g017900.1	2.96	Photosystem I; photosynthesis electron carrier activity
	Solyc10g052740.1	3.01	Photosystem I; photosynthesis electron carrier activity
	Solyc11g007200.1	1.04	Chloroplast inner membrane positive regulation of flavonoid biosynthetic process
	Solyc12g027550.1	1.99	Photosynthetic electron transport in photosystem II
	Solyc12g032970.1	2.69	Photosystem I
	Solyc12g038080.1	2.66	Photosynthetic electron transport in photosystem II
	Solyc10g017940.1	2.53	Photosynthesis, light reaction
	Solyc12g032960.1.	2.56	Photosystem I
	Solyc01g007500.2	2.10	Photosystem II; photosynthetic electron transport chain
	Solyc01g017320.1	2.66	Magnesium ion binding electron carrier activity photosystem I
	Solyc10g017890.1	2.71	Photosynthetic membrane metal ion binding
Chloroplast	Solyc01g006540.2	−1.22	Iron ion binding oxidation-reduction process
	Solyc01g007280.2	1.54	Structural constituent of ribosome
	Solyc01g007330.2	1.27	Magnesium ion binding reductive pentose-phosphate cycle
	Solyc01g007370.2	1.71	Hydrogen ion transmembrane transporter activity; chloroplast inner membrane
	Solyc01g007450.1	1.90	Structural constituent of ribosome
	Solyc01g007470.1	1.68	Structural constituent of ribosome
	Solyc01g007480.1	1.85	Structural constituent of ribosome
	Solyc01g007560.2	1.44	DNA-directed RNA polymerase activity
	Solyc01g007580.2	1.50	Structural constituent of ribosome
	Solyc01g007610.2	1.67	Structural constituent of ribosome
	Solyc01g007620.2	4.63	Structural constituent of ribosome
	Solyc01g007640.2	2.00	ATP binding chromoplast stroma
	Solyc01g007680.1	3.40	Mitochondrion translation initiation factor activity
	Solyc01g007720.2	4.24	Chloroplast
	Solyc01g103920.2	−1.79	Electron carrier activity chloroplast; ferredoxin
	Solyc02g011770.1	1.86	NADH dehydrogenase quinone binding
	Solyc02g067050.2	−1.56	chloroplast
	Solyc03g013600.1	1.70	NADH dehydrogenase quinone binding
	Solyc05g041360.1	2.36	RNA binding
	Solyc09g011150.1	5.74	Chloroplast
	Solyc09g050120.1	3.86	Translation initiation factor activity
	Solyc09g057580.2	−1.06	Gibberellic acid mediated signalling pathway
	Solyc09g061390.1	2.03	RNA binding
	Solyc10g031560.1	2.43	DNA-directed RNA polymerase activity;
	Solyc10g046870.1	1.49	Pollen development jasmonic acid biosynthetic process ethylene-activated signalling pathway
	Solyc10g047410.1	2.56	Photosynthetic electron transport chain
	Solyc11g021170.1	2.78	Hydrolase activity
	Solyc12g035550.1	2.84	Chloroplast membrane
	Solyc12g036540.1	1.57	Chloroplast membrane
	Solyc12g096910.1	4.09	DNA-directed RNA polymerase activity; chloroplast
	Solyc04g039760.1	3.59	Plastid
	Solyc10g031550.1	4.84	DNA-directed RNA polymerase activity
Sugar synthesis	Solyc07g043480.1	1.19	UDP-glucosyl transferase
	Solyc06g072640.1	1.44	Bidirectional sugar transporter
	Solyc02g086650.2	1.26	Glucose-6-phosphate translocator
	Solyc01g073640.2	1.45	Glucose/ribitol dehydrogenase
	Solyc01g080680.2	1.65	Sugar:proton symporter activity

Figure 3. Quantitative real-time PCR validation of RNA-Seq results. Three genes were randomly selected: Solyc01g017310.1.1 (A), Solyc10g052740.1.1 (B) and Solyc01g007350.2.1 (C). Actin was used as the internal control gene.