Raw data for: Dual-cycle CO2 fixation enhances growth and lipid synthesis in Arabidopsis thaliana
Data files
Aug 29, 2025 version files 16.14 GB
-
adp3528_Raw_data.zip
16.14 GB
-
README.md
61.21 KB
Abstract
Carbon fixation through the Calvin-Benson-Bassham (CBB) cycle accounts for the majority of CO2 uptake from the atmosphere. The CBB cycle generates C3 carbohydrates but is inefficient at producing acetyl-CoA (C2), which is the universal precursor for synthesizing lipids. Here, we introduce in Arabidopsis thaliana a new-to-nature CO2 fixing cycle, Malyl-coA-glycerate (McG) cycle, which, together with the CBB cycle, forms a dual-cycle CO2 fixation system. This cycle can fix one additional carbon by phosphoenolpyruvate carboxylase and convert the photorespiration product, glycolate, to acetyl-CoA. Plants with the McG cycle show enhanced protein abundance in their photosystems and enhanced photosystem II efficiency. McG plants had doubled CO2 fixation rates under atmospheric CO2, increased lipid production, pronounced growth enhancement, and tripled the seed yield.
Dataset DOI: 10.5061/dryad.h9w0vt4vf
Description of the data and file structure
The adp3528_Raw_data.zip file contains data for generating figures and tables in "Dual-cycle CO2 fixation enhances growth and lipid synthesis in Arabidopsis thaliana" by Lu et al., 2025. The Fig.1 to 5 are used for generating the main figures Fig.1 to Fig. 5. The data in Fig.S1 to Fig. S32 are used to generate supplementary figures FigS1 to FigS32. The data in TableS1 to TableS7 are used for generating supplementary tables TableS1 to TableS7. The plants used in this study are Arabidopsis wild-type (WT) plants, Arabidopsis transgenic plants expressing complete McG (McG_1, McG_2, McG_3, McG_4), plants expressing partial McG for catalyzing PEP and CO2 to acetyl-coA and glyoxylate (Mc_1, Mc_2, Mc_3), plants expressing partial McG for catalyzing glyoxylate to glycerate (G_1, G_2, G_3), and plants expressing McG without GDH (McG-GDH_1, McG-GDH_2, McG-GDH_3). Their growth phenotypes were imaged at different days after plant germination, at different light periods, on argar plates, under greenhouse without temperature controls, under ambient CO2 (400 ppm) and high CO2 (3000 ppm), under normal light intensity (100 uE) and higher light intensities (150 and 300 uE). Light micrographs of mesophyll cells, scanning electron micrographs of shoot apical meristem with leaf primordia, transmission electron micrographs of leaf and seed sections, confocal images of lipid droplets in leaves are taken by using WT and McG plants. Photosynthetic carbon assimilation rate, light-response carbon assimilation rate, and quantum efficiency of photosystem II of the WT, McG, Mc, G, and McG-GDH plants are measured by LI-COR LI6800. The lipid analyses and proteomic analyses data of the WT and the McG plants are generated by using R, which R scripts and the raw data excel files are provided in the same folder. Statistical analyses are performed by using GraphPad Prism 10.3.0.
File: adp3528_Raw_data.zip
Description: The file contains Fig. 2- Fig. 5 for generating the main figures in the main text, Fig. S1-S26 and Table S1-S7 for the figures and tables in supplementary materials.
Fig2 folder:
(1) The file Fig2_A.csv contains fresh weight (FW) mg of 2-week-old WT and four McG line plants (McG_1,_2,_3,_4)
Number of variables: 5
Variable list:
- genotype: wild-type (WT), McG_1, McG_2, McG_3, McG_4
- bio-rep: 4 biological repeats
- FW mg: fresh weight (milligram; mg)
- AVG: average of fresh weight
- SE: standard error of mean
Statistical analysis: Shapiro-Wilk test for data normality test. Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value
(2) The file Fig2_B.csv contains rosette leaf area of 4-week-old WT and four McG line plants (McG_1,_2,_3,_4)
Number of variables: 5
Variable list:
- genotype: wild-type (WT), McG_1, McG_2, McG_3, McG_4
- bio-rep: 1-5 biological repeats
- rosette leaf area (cm2)
- AVG cm2: average of rosette leaf area (cm2)
- SE: standard error of mean
Statistical analysis: Shapiro-Wilk test for data normality test. Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value
(3) The file Fig2_C.csv contains dry weight (mg) of 4-week-old WT and four McG line plants (McG_1,_2,_3,_4)
Number of variables: 5
Variable list:
- genotype: wild-type (WT), McG_1, McG_2, McG_3, McG_4
- bio-rep: 1-4 biological repeats
- DW mg: dry weight (milligram; mg)
- AVG: average of dry weight
- SE: standard error of mean
Statistical analysis: Shapiro-Wilk test for data normality test. Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value
(4) The file Fig2_D.csv contains dry weight (mg) of 6-week-old WT and four McG line plants (McG_1,_2,_3,_4)
Number of variables: 5
Variable list:
- genotype: wild-type (WT), McG_1, McG_2, McG_3, McG_4
- bio-rep: 9-13 biological repeats
- DW mg: dry weight (milligram; mg)
- AVG: average of dry weight
- SE: standard error of mean
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value
(5) The file Fig2_E.csv contains the rosette leaf number of the 6-week-old plants of 6-week-old WT and four McG line plants (McG_1,_2,_3,_4)
Number of variables: 5
Variable list:
- genotype: wild-type (WT), McG_1, McG_2, McG_3, McG_4
- bio-rep: 4 biological repeats
- leaf number: rosette leaf number of a plant
- AVG: average of rosette leaf number of a plant
- SE: standard error of mean
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value
(6) Fig.2F_WT, _McG1, _McG2, _McG_3, _McG4 are images of individual rosette leaves from 6-week-old WT and McG plants
Fig.2G.csv contains the silique number from the primary inflorescence of the WT and McG plants at 14 days after fertilization (DAF)
Number of variables: 5
Variable list:
- genotype: wild-type (WT), McG_1, McG_2, McG_3, McG_4
- bio-rep: 6 biological repeats
- silique per shoot: silique number from the primary inflorescence
- AVG: average of silique number from the primary inflorescence
- SE: standard error of mean
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value
(7) Fig.2H.csv is the representive image of siliques from the primary inflorescence of the WT and McG plants
(8) Fig.2I.csv contains the seed number per silique of WT and McG plants
Number of variables: 5
Variable list:
- genotype: wild-type (WT), McG_1, McG_2, McG_3, McG_4
- bio-rep: 6 biological repeats
- Seeds per silique: seed number per silique
- AVG: average of seed number per silique
- SE: standard error of mean
Statistical analysis: Shapiro-Wilk test for data normality test. Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value
(9) Fig.2J.csv contains the seed weight per seed of WT and McG plants. Seed weight was calculated as total seed weight divided by the number of seeds per plant
Number of variables: 5
Variable list:
- genotype: wild-type (WT), McG_1, McG_2, McG_3, McG_4
- bio-rep: 5 biological repeats
- seed weight ug/seed: weight (microgram) per seed
- AVG: average of weight (microgram) per seed
- SE: standard error of mean
Statistical analysis: Shapiro-Wilk test for data normality test. Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value
(10) Fig.2J.csv contains the number of seeds per plant
Number of variables: 5
Variable list:
- genotype: wild-type (WT), McG_1, McG_2, McG_3, McG_4
- bio-rep: 5 biological repeats
- seed number : seed number per plant
- AVG: average of seed number per plant
- SE: standard error of mean
Statistical analysis: Shapiro-Wilk test for data normality test. Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value
Fig3 folder:
(1) "Fig3A.csv" is used for analyzing carbon assimilation rates of WT and four McG lines.
Number of variables: 5
Variables:
- Four genotypes: WT, McG_1, McG_2, McG_3, McG_4
- AVG Ci: Average of intercellular concentration of CO2 (µmol mol⁻¹; Ci) from three measurements of three plant replicates
- SE Ci: standard errors of intercellular concentration of CO2 (µmol mol⁻¹; Ci) from three measurements of three plant replicates
- AVG A: Average of net carbon assimilation rate (µmol m⁻² s⁻¹; A) from three measurements of three plant replicates
- SE A: standard errors of net carbon assimilation rate (µmol m⁻² s⁻¹; A) from three measurements of three plant replicates
(2) Fig3B.csv contains A400 (CO2 umol m-2s-1) of WT and four McG lines.
Number of Variables: 4
Variables:
- genotype: WT, McG_1, McG_2, McG_3, McG_4
- bio-rep: 3 biological replicate for WT and each McG line
- A400: net carbon assimilation rate measured under CO2 concentration of 400 umol mol-1.
- AVG: average of A400 of biological replicates
- SE: standard error of mean of A400 of biological replicates
(3) Fig3C.csv contains Amax (CO2 umol m-2s-1) of WT and four McG lines.
Number of Variables: 4
Variables:
- genotype: WT, McG_1, McG_2, McG_3, McG_4
- bio-rep: 3 biological replicate for WT and each McG line
- Amax: maximal net carbon assimilation rate (Amax) measured under CO2 concentrations higher then 1200 umol mol-1.
- AVG: average of Amax of biological replicates
- SE: standard error of mean of Amax of biological replicates
(4) "Fig3D.csv" is used for determining CO2 compensation points (Ci*) for WT and McG plants.
Number of variables: 5
Variables:
- Four genotypes: WT, McG_1, McG_2, McG_3, McG_4
- repeats: three biological repeats from each line
- Ci* (umol mol-1): CO2 compensation points (Ci*) for WT and McG plants
- AVG: average values of CO2 compensation points (Ci*)
- SE: standard errors of means of CO2 compensation points (Ci*)
(5) "Fig3E.csv" contains data net CO2 assimilation rates at various light intensities were measured under ambient CO2 (400 ppm) for plants grown under ambient CO2 condition.
Number of variables: 6
Variables:
- Four genotypes: WT, McG_1, McG_2, McG_3, McG_4
- repeats: four biological repeats from each line
- Qin (µmol m⁻² s⁻¹): various light intensities from 1500 µmol m⁻² s⁻¹ to 0 µmol m⁻² s⁻¹
- A (µmol m⁻² s⁻¹): net carbon assimilation rate
- AVG: average A values of four biological repeats
- SE: standard errors of means of A values of four biological repeats
(6) "Fig3F.csv" file contains the net CO2 assimilation rates at various light intensities were measured under 1500 ppm CO2 for plants grown under high CO2 (3000ppm) condition
Number of variables: 6
Variables:
- Four genotypes: WT, McG_1, McG_2, McG_3, McG_4
- repeats: four biological repeats from each line
- Qin (µmol m⁻² s⁻¹): various light intensities from 1500 µmol m⁻² s⁻¹ to 0 µmol m⁻² s⁻¹
- A (µmol m⁻² s⁻¹): net carbon assimilation rate
- AVG: average A values of four biological repeats
- SE: standard errors of means of A values of four biological repeats
Fig4 folder:
(1) "Fig4A.csv" file contains 13CO2 incorporation data into metabolites of McG cycle and carbohydrate precursor glucose-1-phosphate (G1P) in WT and McG plants
Number of variables: 5
Variables:
- Four genotypes: WT, McG_1, McG_2, McG_3, McG_4
- Six metabolites: G1P: glucose-1-phosphate; PEP: phosphoenolpyruvate; malate, Tartonic semialdehyde; 2PG: 2-phosphoglycerate; acetyl-coA.
- 13C/12C: The ratio of 13C-labelled to 12C-unlabelled metabolite. M1: one carbon molecule of above metabolite is 13C-labeled; M2: two carbon molecules of above metabolite are 13C-labeled; M3: three carbon molecules of above metabolite are 13C-labeled; M4: four carbon molecules of above metabolite are 13C-labeled; M5: five carbon molecules of above metabolite are 13C-labeled; M6: six carbon molecules of above metabolite are 13C-labeled.
- AVG: average value of 13C/12C ratios from 6 biological replicates of each line.
- SE: standard errors of of 13C/12C ratios from 6 biological replicates of each line.
- 13C/12C (total): Sum of 13C /12C ratios for each line for statistical analysis of significance difference between WT and McG lines.
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value
(2) "Fig4B.csv" file contains data acquired from GC-MSMS analytic experiments, which are used for determining the contents of the photorespiration metabolites.
Number of variables: 5
Variables:
- genotypes: WT, McG_1, McG_2, McG_3, McG_4
- bio-rep: 5-6 biological replicates
- metabolite/ribitol ratio: the peak area of the metabolite to the peak area of the ribitol. Metabolites are glycolate, glyoxylate, serine, glycin, glycerate, and pyruvate.
- AVG: average value of metabolite/ribitol ratios of biological replicates
- SE: standard error of metabolite/ribitol ratios of biological replicates
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value
Fig5 folder:
(1) The first folder (Fig. 5A Nile red staining leaves) contains images acquired from a confocal microscopy experiment for visualizing lipid droplets in leaves.
(2) The folder " Fig5B Leaf TEM LD" contains transmission electron micrographs (TEM) of the leaves for visualizing lipid droplets (LD) in the WT and McG lines.
(3) The folder "Fig5C green seed TEM" contains TEMs acquired from green seeds of each line for visualizing their seed LDs.
(4) The file " Fig5D.csv" contains the concentrations of different lipid classes in the leaves of the WT and the McG plants."LipidBarByClass.R", is used to calculate the concentration of each lipid class.
Number of variables: 3
Variables:
- genotypes: WT, McG_1, McG_2, McG_3, McG_4
- bio-rep: 5-6 biological replicates
- Lipid class: TAG: triacylglycerol; MGDG: monogalactosyldiacylglycerol; DGDG: digalactosyldiacylglycerol; FA: fatty acid. Concentration unit: ug g-1 Fw
Statistical analysis:
Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05)
Dunnett's T3 multiple comparisons test for adjusted-P-value
(5) The file "Fig5E.csv" contains the data for analyzing chain length distribution in triacylglycerol (TAG) by R coding file "LipidFADis.R".
Number of variables: 2
- genotype and biological replicates: WT_1 to WT_6 (six biological replicates for WT), McG1_1, McG1_3, McG1_4, McG1_5, McG1_6 (five biological replicates for McG_1 line), McG2_1 to McG2_6 (six biological replicates for McG_2 line), McG3_1 to McG3_6 (six biological replicates for McG_3 line), McG4-1 to McG4-6 (six biological replicates for McG_4 line).
- TG chain lengths: concentrations of different chain lengths in each triacylglycerol (TG)
(6) The file "Fig5F.csv" contains the data for the concentrations of different lipid classes in the seeds of the WT and the McG plants."LipidBarByClass.R", is used to calculate the concentration of each lipid class.
Number of variables: 3
Variables:
- genotypes: WT, McG_1, McG_2, McG_3, McG_4
- bio-rep: 5-6 biological replicates
- Lipid class: TAG: triacylglycerol; DAG: diacylglycerol; PC: phosphatidylcholine; FA: fatty acid. Concentration unit: ug g-1 Fw
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value
(7) The file "Fig5G.csv" contains the data for analyzing chain length distribution in triacylglycerol (TAG) of the seeds from WT and McG lines, by using R coding file "LipidFADis.R".
Number of variables: 2
- genotype and biological replicates: WT_1 to WT_6 (six biological replicates for WT), McG1_1 to McG_1_6 (six biological replicates for McG_1 line), McG_2_1 to McG_2_6 (six biological replicates for McG_2 line), McG_3_1 to McG_3_6 (six biological replicates for McG_3 line), McG_4-1 to McG_4-6 (six biological replicates for McG_4 line).
- TG chain lengths: concentrations of different chain lengths in each triacylglycerol (TG)
FigS2 folder:
(1) The file "FigS2A.csv" showed that expression of MTK fusion protein and MCL can rescue the growth defect of the acetyl-coA auxotrophic ˆstrain (LYN2-1), which cannot metabolize glucose to acetyl-coA for growth.
Number of variables: 3
Variables:
- genotypes: E. coli LYN2-1strain and the E. coli LYN2-1strain expressing with MTK fusion protein and MCL (1, 12, 17, 19)
- incubation time (h: hour): 0, 24, 48, 72h
- OD600: absorption at 600 nm wavelength at different incubation time point (0, 24, 48, 72h)
(2) The file "FigS2B_Mc_plasmid_pCambia1300-35S-1B-3FLAG-PPC_Acc65I-35S__1B-A-B_35S__1B-Mcl-Xba1 Correct nanopor rapid.fasta" and "FigS2B_G_plamid_map_pEarleygate103-U10p-1B-CrGDH-1B-Gcl-1B-Tsr.fasta" contain the maps of the Mc and G constructs.
(3) The files "FigS2C_GDH_GCL_TSR_Untitled 55", "FigS2C_PPC_MTK_MCL_Untitled 42", and "FigS2C_loading_CBS_IMG_5768" are the images acquired from immunoblotting to show protein expressions of the McG transgenes in the Mc and G transgenic lines.
FigS3 folder:
(1) The file "FigS3A.csv" demonstrated the transcript levels of the McG transgenes in the McG lines. Total RNA isolated from 2-week-old WT and McG plants and used for digital qPCR to quantitate the transcript levels of PPC, MtKA-B, Mcl, GDH, Gcl and Tsr. The expression of the endogenous granule-bound starch synthase (GBSS) gene was used as the internal control.
Number of variables: 5
Variables:
- genotype: WT. McG_1, McG_2, McG_3, McG_4
- bio-rep: 3 biological replicates for each line
- Transcript levels of PPC, MtkA_B, Mcl, GDH, Gcl, and *Tsr *to the transcript level of endogenous GBSS: PPC/GBSS, MTK/GBSS, MCL/GBSS, GDH/GBSS, GCL/GBSS, and TSR/GBSS.
- AVG: average transcriptional level of three biological replicates
- SE: standard error of mean of transcriptional level of three biological replicates.
(2) The file "FigS3B_individual_McG_plants_Untitled-1", "FigS3B_loading_CBS_IMG_4358" showed the protein expression levels of the McG transgenes in the WT and McG lines.
(3) The folder "FigS3C_nonopore WT McG" contains raw reads (.fasta files) acquired from Nanopore whole genome sequencing for the WT and the McG lines.
FigS4 folder:
The file "FigS4_McG-GDH_Untitled 45-1.tif" contains immunoblotting results for the detection of heterologous PPC, MTK, MCL, GCL, and TSR protein expression in McG-GDH lines. The file "FigS4_loading_CBS_IMG_5771_1.tif" for loading control.
FigS5 folder:
This folder contains photographs of the WT and McG plants for 4 weeks, 6 weeks, and 7 weeks.
FigS6 folder:
This folder contains photographs of WT (white label), selected F3 homozygous McG_1 (pink), McG_2 (yellow/orange), McG_3 (green), McG_4 (blue) plants.
FigS7 folder:
(1) The subfolders " FigS7A_10d", " FigS7A_6_7wk", "FigS7A_9wk", "Fig.S7B", "FigS7C_4wk", "FigS7C_6wk", and "FigS7D_6wk" contain images for showing growth phenotypes of WT and McG plants in FigS7A, FigS7B, FigS7C, and FigS7D.
(2) The file "FigS7C_6wk.csv" in the "FigS7C_6wk" folder contains the fresh weight (FW) and the dry weight (DW) of 6-week-old WT and McG plants.
Number of variables: 8
Variables:
- genotype: WT. McG_1, McG_2, McG_3, McG_4
- bio-rep: 9-13 biological replicates for each line
- FW (g): fresh weight (gram)
- FW AVG: average FW of biological replicates
- FW SE: standard error of mean FW of biological replicates
- DW (mg): dry weight (milligram)
- DW AVG: average DW of biological replicates
- DW SE: standard error of mean DW of biological replicates
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value
(3) The file "FigS7D.csv" in the "FigS7D_6wk" folder contains the fresh weight (FW) and the dry weight (DW) of 6-week-old WT and McG plants.
Number of variables: 8
Variables:
- genotype: WT. McG_1, McG_2, McG_3, McG_4
- bio-rep: 8 biological replicates for each line
- FW (g): fresh weight (gram)
- FW AVG: average FW of biological replicates
- FW SE: standard error of mean FW of biological replicates
- DW (mg): dry weight (milligram)
- DW AVG: average DW of biological replicates
- DW SE: standard error of mean DW of biological replicates
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
FigS8 folder:
This folder contains photographs of the WT and McG plants for 4, 6, and 9 weeks under greenhouse conditions.
FigS9 folder:
This folder contains photographs of the WT and McG plants grown under 8h light/16h dark (8_16) short day or 16h light/ 8h dark (16_8) long day conditions.
FigS10 folder:
(1) The file "FigS10A_leaf primordia.pptx" contains scanning electron micrographs of shoot apical meristems from the WT and McG plants.
(2) The file "FigS10B_longitudinal SAM_Highlight phenotype Arabidopsis shoot apical meristem LM.pptx" contains light micrographs of longitudinal shoot apical meristems for the WT and the McG plants.
(3) The file "FigS10C.csv" contains raw data for calculating leaf emergence rates of the WT and McG lines.
Number of variables: 4
Variables:
- genotype: WT. McG_1, McG_2, McG_3, McG_4
- bio-rep: 5-7 biological replicates for each lines
- DAG: days after germination
- leaf number: rosette leaf number per plant
FigS12 folder:
(1) The folder "FigS12AB_opensilique_seeds" contains light micrographs of green open siliques and their seeds from the WT and McG lines.
(2) The folder "FigS12C_green seed blightfield" contains light micrographs of the green seeds from the WT and McG lines.
(3) The folder "FigS12D_mature seed BF" contains the micrographs of the mature seeds from the WT and the McG lines.
(4) The file "FigS12E_csv" contains raw data for calculating seed germination rates of the WT and McG lines.
Number of variables: 4
Variables:
- genotype: WT. McG_1, McG_2, McG_3, McG_4
- bio-rep: 4 plate replicates for each lines
- initial seed number: number of seeds on each plate
- hr after sow: hour after sowing seeds under 12hr/12hr light/dark cycle, light intensity of 100 𝜇mol m-2 s-1
- germination number: number of seeds are germinated
- %: germination rate: % of germination number/initial seed number
- AVG: average germination rate from 4 plate replicates of each line
- SE: standard error of mean of germination rate from 4 plates of each line
FigS13 folder:
This folder contains photographs for 9-week-old and 3-month-old WT and McG plants
FigS14 folder:
(1) The folder "FigS14A_leaf cross section" contains cross-section light micrographs of 2-week-old leaves from the WT and McG lines.
(2) The file "FigS14B.csv" contains raw data for calculating the proportion of each ploidy number (2C-16C) of the WT and McG lines.
Number of variables: 17
Variables:
- genotype: WT. McG_1, McG_2, McG_3, McG_4
- bio-rep: 4 biological replicates for each lines
- proportion of each ploidy: proportion of 2C (diploid), proportion of 4C (diploid number of 2), proportion of 8C (diploid number of 4), proportion of 16C (diploid number of 8), and proportion of 32C (diploid number of 16).
- 2C AVG: averaged diploid number of 4 biological replicates for each line
- 2C SE: standard error of mean of diploid number of 4 biological replicates for each line
- 4C AVG: averaged 4C of 4 biological replicates for each line
- 4C SE: standard error of mean of 4C of 4 biological replicates for each line
- 8C AVG: averaged 8C of 4 biological replicates for each line
- 8C SE: standard error of mean of 8C of 4 biological replicates for each line
- 16C AVG: averaged 16C of 4 biological replicates for each line
- 16C SE: standard error of mean of 16C of 4 biological replicates for each line
- 32C AVG: averaged 32C of 4 biological replicates for each line
- 32C SE: standard error of mean of 32C of 4 biological replicates for each line
FigS15 folder:
(1) The folder "FigS15A_14d root" contains photographs of 14-day-old seedlings of the WT and McG lines.
(2) The file "FigS15B.csv" contains raw data for root weights of the WT and McG lines.
Number of variables: 5
Variables:
- genotype: WT. McG_1, McG_2, McG_3, McG_4
- no: 6 biological replicates for each line
- mg: milligram of root weight of each plant
- AVG: average of root weight of 6 biological replicates
- SE: standard error of mean of root weight of 6 biological replicates
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value<0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
(3) The file "FigS15C_IMG_5395" represents 7-week-old root phenotypes of the soil-grown WT and McG lines.
FigS16 folder:
This folder contains two replicate experiments of Fig. S15A
FigS17 folder:
(1) The file "FigS17_ABCD.csv_contains raw data of the fresh weight (FW) and dry weight (DW) of 4-week-old WT, McG, Mc, G, and McG-GDH lines.
Number of variables: 8
Variables:
- genotype: WT, McG_1, McG_2, McG_3, McG_4, Mc_1, Mc_2, Mc_3, G_1, G_2, G_3, McG-GDH_1, McG-GDH_2, McG-GDH_3
- no: 6 biological replicates for each line
- FW mg: milligram of fresh weight of a plant
- FW AVG: average fresh weight of 6 biological replicates
- FW SE: standard error of mean of FW of 6 biological replicates
- DW mg: milligram of dry weight of a plant
- DW AVG: average dry weight of 6 biological replicates
- DW SE: standard error of mean of DW of 6 biological replicates
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
(2) The file "FigS17BD statistics.ppt" contains adjusted p-values between multiple lines by using One-way Welch’s ANOVA test, followed by Dunnett’s T3 multiple pairwise comparison.
(3) The images "FigS17E_2wk_IMG_5696.jpeg", "FigS17E_3wk_IMG_5724.jpeg", and "FigS17E_4wk_IMG_5752" represent the growth phenotypes of the lines for 2-week, 3-week, and 4-week-old under ambient CO2 condition.
FigS18 folder:
There are four replicate experiments of Fig.S17, labeled as "FigS18A_1_3wk", "FigS18B_1_3wk", "FigS18C_4_7wk", and "FigS18D_4wk".
(1) These four folders contain images showing growth phenotypes of WT, McG, Mc, G, and McG-GDH lines under ambient CO2 condition.
(2) The file "FigS18D.csv" in the FigS18D_4wk contains FW and DW of 32-day-old WT, McG, Mc, G, and McG-GDH plants under ambient CO2, light intensity of 100 𝜇mol m-2 s-1 (100uE).
Number of variables: 8
Variables:
- genotype: WT, McG_1, McG_2, McG_3, McG_4, Mc_1, Mc_2, G_1, G_2, McG-GDH_1, McG-GDH_2
- bio-rep: 8 biological replicates for each line
- FW g: gram of fresh weight of a plant
- FW AVG: average fresh weight of 8 biological replicates
- FW SE: standard error of mean of FW of 8 biological replicates
- DW mg: milligram of dry weight of a plant
- DW AVG: average dry weight of 8 biological replicates
- DW SE: standard error of mean of DW of 8 biological replicates
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
FigS19 folder:
(1) The file "FigS19ABCD.csv" contains raw data of the FW and DW of the WT, McG, Mc, G, and McG-GDH lines under high CO2 (3000 ppm) conditions.
Number of variables: 8
Variables:
- genotype: WT, McG_1, McG_2, McG_3, McG_4, Mc_1, Mc_2, Mc_3, G_1, G_2, G_3, McG-GDH_1, McG-GDH_2. McG-GDH_3
- bio-rep: 6 biological replicates for each line
- FW mg: milligram of fresh weight of a plant
- FW AVG: average fresh weight of 6 biological replicates
- FW SE: standard error of mean of FW of 6 biological replicates
- DW mg: milligram of dry weight of a plant
- DW AVG: average dry weight of 6 biological replicates
- DW SE: standard error of mean of DW of 6 biological replicates
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
Table of adjusted-P-value for FW
Table of adjusted-P-value for DW
(2) The folders "FigS19E_2wk_111224 3000" and "FigS19E_4wk_271224 3000" contain photographs of the WT, McG, Mc, G, and McG-GDH lines for 2-week-old and 4-week-old plants.
FigS20 folder:
The replicate experiment of Fig. S19E for growth phenotype observations.
FigS21 folder:
(1) The folder "FigS21A_150E" contains photographs of the plants grown under 150 uE light intensity for 2-4 weeks.
(2) The folder "FigS21B_300E" contains photographs of the plants grown under 300 uE light intensity for 2-4 weeks.
(3) The file "FigS21A_150E.csv" in the 4weekold subfolder of the FigS21A_150E folder contains FW and DW of the 4-week-old plants under light intensity of 150 𝜇mol m-2 s-1 (150 μE).
Number of variables: 8
Variables:
- genotype: WT, McG_1, McG_3, Mc_1, Mc_2, G_1, G_2, McG-GDH_1, McG-GDH_2.
- bio-rep: 8 biological replicates for each line
- FW g: gram of fresh weight of a plant
- FW AVG: average fresh weight of 8 biological replicates
- FW SE: standard error of mean of FW of 8 biological replicates
- DW mg: milligram of dry weight of a plant
- DW AVG: average dry weight of 8 biological replicates
- DW SE: standard error of mean of DW of 8 biological replicates
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
Table of adjusted-P-value for FW
Table of adjusted-P-value for DW
(4) The file "FigS21B_300E.csv" in the 4weekold subfolder of the FigS21B_300E folder contains FW and DW of the 4-week-old plants under light intensity of 300 𝜇mol m-2 s-1 (300 μE)
Number of variables: 8
Variables:
- genotype: WT, McG_1, McG_3, Mc_1, Mc_2, G_1, G_2, McG-GDH_1, McG-GDH_2.
- bio-rep: 8 biological replicates for each line
- FW g: gram of fresh weight of a plant
- FW AVG: average fresh weight of 8 biological replicates
- FW SE: standard error of mean of FW of 8 biological replicates
- DW mg: milligram of dry weight of a plant
- DW AVG: average dry weight of 8 biological replicates
- DW SE: standard error of mean of DW of 8 biological replicates
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
Table of adjusted-P-value for FW
Table of adjusted-P-value for DW
FigS22 folder:
(1) The "FigS22A.csv" file contains net carbon assimilation rates (A400 [CO2 µmol m⁻² s⁻¹] ) of 4-week-old WT and McG plant leaves under ambient CO2 (400 ppm)
Number of variables: 3
Variables:
- genotype: WT, McG_1, McG_2, McG_3, McG_4
- leaf number: 10th, 12th, 14th leaves of WT and McG plants are used for A400 measurements
- A400 (µmol m⁻² s⁻¹): net carbon assimilation rate at ambient CO2 (400 ppm)
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
(2) The "FigS22B.csv" file contains leaf mass per area (LMA; g m-2) of 10th, 12th, 14th leaves from 4-week-old WT and McG plants grown under ambient CO2 (400 ppm)
Number of variables: 3
Variables:
- genotype: WT, McG_1, McG_2, McG_3, McG_4
- leaf number: 10th, 12th, 14th leaves of WT and McG plants
- LMA (g m⁻²¹): leaf mass per area (LMA; g m-2)
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
(3) The "FigS22C.csv" file contains chlorophyll content (g m-2) of 10th, 12th, 14th leaves from 4-week-old WT and McG plants grown under ambient CO2 (400 ppm)
Number of variables: 3
Variables:
- genotype: WT, McG_1, McG_2, McG_3, McG_4
- leaf number: 10th, 12th, 14th leaves of 4-week-old WT and McG plants
- chlorophyll content (g m⁻²): chlorophyll content of 10th, 12th, 14th leaves of 4-week-old WT and McG plants
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
(4) The "FigS22D.csv" file contains A400 ( CO2 µmol m⁻² s⁻¹) normalized to LMA (g m-2) of 10th, 12th, 14th leaves from 4-week-old WT and McG plants grown under ambient CO2 (400 ppm) as to A400/LMA (CO2 µmol g⁻1 s⁻¹)
Number of variables: 3
Variables:
- genotype: WT, McG_1, McG_2, McG_3, McG_4
- leaf number: 10th, 12th, 14th leaves of 4-week-old WT and McG plants
- A400/LMA : A400 normalized to LMA of 10th, 12th, 14th leaves of 4-week-old WT and McG plants
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
(5) The "FigS22E.csv" file contains A400 ( CO2 µmol m⁻² s⁻¹) normalized to chlorophyll content (g m-2) of 10th, 12th, 14th leaves from 4-week-old WT and McG plants grown under ambient CO2 (400 ppm) as to A400/chll (CO2 µmol g⁻1 s⁻¹)
Number of variables: 3
Variables:
- genotype: WT, McG_1, McG_2, McG_3, McG_4
- leaf number: 10th, 12th, 14th leaves of 4-week-old WT and McG plants
- A400/Chll : A400 normalized to chlorophyll contents of 10th, 12th, 14th leaves of 4-week-old WT and McG plants
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
FigS23 folder:
(1) The file "FigS23A.csv" contains net carbon assimilation rates (A400 [CO2 µmol m⁻² s⁻¹] ) of 5-week-old WT and McG plant leaves under ambient CO2 (400 ppm)
Number of variables: 3
Variables:
- genotype: WT, McG_1, McG_2, McG_3, McG_4
- leaf number: 10th, 12th, 14th, 16th leaves of WT and McG plants are used for A400 measurements
- A400 (µmol m⁻² s⁻¹): net carbon assimilation rate at ambient CO2 (400 ppm)
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
(2) The "FigS23B.csv" file contains leaf mass per area (LMA; g-1 m-2) of 10th, 12th, 14th leaves from 5-week-old WT and McG plants grown under ambient CO2 (400 ppm)
Number of variables: 3
Variables:
- genotype: WT, McG_1, McG_2, McG_3, McG_4
- leaf number: 10th, 12th, 14th, 16th leaves of WT and McG plants
- LMA (g m⁻²¹): leaf mass per area (LMA; g-1 m-2)
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
(3) The "FigS23C.csv" file contains chlorophyll content (g-1 m-2) of 10th, 12th, 14th, 16th leaves from 5-week-old WT and McG plants grown under ambient CO2 (400 ppm)
Number of variables: 3
Variables:
- genotype: WT, McG_1, McG_2, McG_3, McG_4
- leaf number: 10th, 12th, 14th, 16th leaves of 5-week-old WT and McG plants
- chlorophyll content (g m⁻²): chlorophyll content of 10th, 12th, 14th, 16th leaves of 5-week-old WT and McG plants
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
(4) The "FigS23D.csv" file contains A400 ( CO2 µmol m⁻² s⁻¹) normalized to LMA (g-1 m-2) of 10th, 12th, 14th, 16th leaves from 5-week-old WT and McG plants grown under ambient CO2 (400 ppm) as to A400/LMA (CO2 µmol g⁻1 s⁻¹)
Number of variables: 3
Variables:
- genotype: WT, McG_1, McG_2, McG_3, McG_4
- leaf number: 10th, 12th, 14th leaves of 5-week-old WT and McG plants
- A400/LMA : A400 normalized to LMA of 10th, 12th, 14th, 16th leaves of 5-week-old WT and McG plants
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
(5) The "FigS23E.csv" file contains A400 ( CO2 µmol m⁻² s⁻¹) normalized to chlorophyll content (g-1 m-2) of 10th, 12th, 14th, 16th leaves from 5-week-old WT and McG plants grown under ambient CO2 (400 ppm) as to A400/chll (CO2 µmol g⁻1 s⁻¹)
Number of variables: 3
Variables:
- genotype: WT, McG_1, McG_2, McG_3, McG_4
- leaf number: 10th, 12th, 14th, 16th leaves of 5-week-old WT and McG plants
- A400/Chll : A400 normalized to chlorophyll contents of 10th, 12th, 14th, 16th leaves of 5-week-old WT and McG plants
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
FigS24 folder:
(1) The "FigS24A.csv" file contains raw data for net carbon assimilation rates of the WT and McG lines under various CO2 concentrations, and light intensity of 100 uE.
Number of variables: 8
Variables:
- genotype: WT, McG_1, McG_2, McG_3, McG_4
- biological replicates: three replicates for WT, four replicates for McG_1, three replicates for McG_2, and four replicates for McG_3 and McG_4
- Ci (CO2 𝜇mol mol-1): intercellular CO2 concentrations (Ci)
- A (CO2 𝜇mol m-2s-1): net carbon assimilation rate
- AVG Ci (CO2 𝜇mol mol-1): average Ci value of biological replicates
- AVG A (CO2 𝜇mol m-2s-1): average A value of biological replicates
- SE Ci (CO2 𝜇mol mol-1): standard error of Ci mean of biological replicates
- SE A (CO2 𝜇mol m-2s-1): standard error of A mean of biological replicates
(2) The "FigS24B.csv" file shows the net carbon assimilation rates under ambient CO2 (400 ppm) as to A400 of WT and McG plants in the FigS24A.csv.
Number of variables: 4
Variables:
- genotype and biological replicates : three replicates for WT, four replicates for McG_1, three replicates for McG_2, and four replicates for McG_3 and McG_4
- A400 (CO2 𝜇mol m-2s-1) under 400ppm CO2: net carbon assimilation rate under 400ppm CO2
- AVG A400 (CO2 𝜇mol m-2s-1): average A value of biological replicates
- SE A400 (CO2 𝜇mol m-2s-1): standard error of A mean of biological replicates
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
(3) The "FigS24C.csv" contains Water use efficiency (WUE) of WT and McG lines under light intensity of 100 𝜇mol m-2s-1, 400 𝜇mol mol-1 of CO2
Number of variables: 6
Variables:
- genotype and biological replicates : three replicates for WT, four replicates for McG_1, three replicates for McG_2, and four replicates for McG_3 and McG_4
- A400 (CO2 𝜇mol m-2s-1) under 400ppm CO2: net carbon assimilation rate under 400ppm CO2
- Emm: transpiration rate (mmol m⁻² s⁻¹) under 400pm CO2
- WUE (A/E) at 400ppm: water use efficiency is calculated as A400/Emm (µmol mmol-1)
- AVG: average WUE value of biological replicates
- SE: standard error of WUE mean of biological replicates
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
(4) The "FigS24D.csv" file contains the day respiration rate of WT and McG lines by using the slope-intercept approach, which has been published by Walker et al, 2016 (reference 47).
Number of variables: 4
Variables:
- genotype and biological replicates : three replicates for WT, McG_1, McG_2, McG_3, and McG_4
- Rd (umol m-2 s-1): day respiration rate
- AVG: average Rd of biological replicates
- SE: standard error of Rd mean of biological replicates
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
(5) The "FigS24E.csv" file contains net carbon assimilation rates of whole plants under various CO2 concentrations.
Number of variables: 8
Variables:
- genotype and biological replicates : four replicates for WT, McG_1, McG_2, McG_3, and McG_4
- rosette area m2: whole rosette area of a plant (m2)
- CO2_a (µmol mol⁻¹): ambient CO2 concentration
- A (µmol m⁻² s⁻¹): net carbon assimilation rate per leaf area
- AVG Ca: average Ca of biological replicates
- SE Ca: standard error of Ca mean of biological replicates
- AVG A: average net carbon assimilation rate per leaf area of biological replicates
- SE A: standard error of A mean per leaf area of biological replicates
FigS25 folder:
(1) The file "FigS25_A.csv" contains net CO2 assimilation rates for the WT and Mc plants under various CO2 concentrations.
Number of variables: 7
Variables:
- genotype and replicates: three biological replicates for WT, Mc_1, Mc_2, and Mc_3 lines
- Ci (µmol mol⁻¹): intercellular CO2 concentrations
- A µmol m⁻² s⁻¹: net carbon assimilation rate
- Ci AVG: average of Ci of biological replicates
- Ci SE: standard error of Ci mean of biological replicates
- A AVG: average of A of biological replicates
- A SE: standard error of A mean of biological replicates
(2) The file "FigS25_B.csv" contains net CO2 assimilation rates for the WT and G plants under various CO2 concentrations.
Number of variables: 7
Variables:
- genotype and replicates: three biological replicates for WT, G_1, G_2, and G_3 lines
- Ci (µmol mol⁻¹): intercellular CO2 concentrations
- A µmol m⁻² s⁻¹: net carbon assimilation rate
- Ci AVG: average of Ci of biological replicates
- Ci SE: standard error of Ci mean of biological replicates
- A AVG: average of A of biological replicates
- A SE: standard error of A mean of biological replicates
(3) The file "FigS25C.csv" contains net CO2 assimilation rates under various CO2 concentrations for the WT and McG-GDH plants.
Number of variables: 7
Variables:
- genotype and replicates: three biological replicates for WT, McG-GDH_1, McG-GDH_2, and McG-GDH_3 lines
- Ci (µmol mol⁻¹): intercellular CO2 concentrations
- A µmol m⁻² s⁻¹: net carbon assimilation rate
- Ci AVG: average of Ci of biological replicates
- Ci SE: standard error of Ci mean of biological replicates
- A AVG: average of A of biological replicates
- A SE: standard error of A mean of biological replicates
(4) The "FigS25D.csv" file contains A400 values for three replicates of WT and Mc_1, Mc_2, and Mc_3 lines showed in "FigS25A.csv"
Number of variables: 4
Variables:
- genotype and replicates: three biological replicates for WT, Mc_1, Mc_2, Mc_3
- A400 (CO2 𝜇mol m-2s-1): net carbon assimilation rate under 400ppm CO2
- AVG: average of A400 of replicates
- SE: standard error of A400 mean of replicates
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
(5) The "FigS25E.csv" file contains A400 values for three replicates of WT and G_1, G_2, and G_3 lines showed in "FigS25B.csv"
Number of variables: 4
Variables:
- genotype and replicates: three biological replicates for WT, G_1, G_2, and G_3 line
- A400 (CO2 𝜇mol m-2s-1): net carbon assimilation rate under 400ppm CO2
- AVG: average of A400 of replicates
- SE: standard error of A400 mean of replicates
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value
(6) The "FigS25F.csv" file contains A400 values for three replicates of WT and McG-GDH_1, McG-GDH_2, and McG-GDH_3 lines showed in "FigS25C.csv"
Number of variables: 4
Variables:
- genotype and replicates: three biological replicates for WT, McG-GDH_1, McG-GDH_2, McG-GDH_3
- A400 (CO2 𝜇mol m-2s-1): net carbon assimilation rate under 400ppm CO2
- AVG: average of A400 of replicates
- SE: standard error of A400 mean of replicates
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
FigS26 folder:
(1) The file " FigS26A.csv" contains the quantum efficiency of PSII under various light intensities (from 1500 μE to 25uE) at 400ppm CO2 for the WT and McG plants grown under ambient CO2 condition.
Number of Variables: 5
Variables:
- genotypes and replicates: four biological replicates for WT, McG_1, McG_2, McG_3, McG_4
- Qin Light µmol m⁻² s⁻¹: light intensity (µmol m⁻² s⁻¹)
- PhiPSII: quantum efficiency of photosystem II
- AVG: average of PhiPSII of biological replicates
- SE: standard error of PhiPSII mean of biological replicates
(2)The file " FigS26B.csv" contains the quantum efficiency of PSII under various light intensities (from 1500 μE to 25uE) at 1500ppm CO2 for the WT and McG plants grown under high CO2 (3000ppm) condition.
Number of Variables: 5
Variables:
- genotypes and replicates: four biological replicates for WT, McG_1, McG_2, McG_3, McG_4
- Qin Light µmol m⁻² s⁻¹: light intensity (µmol m⁻² s⁻¹)
- PhiPSII: quantum efficiency of photosystem II
- AVG: average of PhiPSII of biological replicates
- SE: standard error of PhiPSII mean of biological replicates
FigS27 folder:
(1) The "FigS27AB_photosynthesisHeatmap.csv" contains data for generating heatmaps shown in FigS27A and FigS27B by using "photosynthesisHeatmapSeparate.R"
Variables:
Accession: Uniport ID
protein name
group: a: proteins involved in photosystem II; b: proteins involved in cytochrome b6/f and electron transfer; c: proteins involved in photosystem I; d: proteins involved in F-type ATP synthase; e: proteins involved in Calvin-Benson-Bassham (CBB) cycle
genotype and replicates: four biological replicates for WT, McG_1, McG_2, McG_3, and McG_4 lines.
(2) The "FigS27C.csv" file contains RuBisCO activity measurements of WT and four McG lines grown under ambient CO2 or High CO2 (3000 ppm) condition.
Number of Variables: 5
Variables:
- genotype and replicates: four biological replicates are used for WT and four McG lines.
- growth condition: plants were grown under ambient CO2 or High CO2 (3000 ppm)
- Unit mg-1 protein: Unit enzyme activity per mg protein extract.
- AVG: average unit enzyme activity per mg protein extract of biological replicates
- SE: standard errors of mean of unit enzyme activity per mg protein extract of biological replicates
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
FigS28 folder:
(1) The file "FigS28A.csv" contains quantum efficiency of PSII of WT and McG lines under light intensity of 100 µmol m⁻² s⁻¹, ambient CO2 (400 ppm).
Number of variables: 4
Variables:
- genotype and replicates: four biological replicates for WT and four McG lines
- PhiPSII: quantum efficiency of PSII
- Average: average of PhiPSII
- SE: standard error of PhiPSII mean of biological replicates
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
(2) The file "FIgS28B_LM ppt.ppt" contains light micrographs of the WT and McG leaves.
(3) The file "FigS28C.csv" is used to calculate chloroplast number per mesophyll cell of the WT and McG lines.
Number of variables: 2
Variables:
- genotype and replicates: 80 mesophyll cell replicates for WT and four McG line
- Chloroplast number per mesophyll cell
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
FigS29 folder:
(1) The folders "FigS29A_ WT", "FigS29B_McG_1", "FigS29C_McG*_*2", "FigS29D_McG_3", and "FigS29E_McG_4" contain transmission electron micrographs of cross-section leaves for WT and each McG line accordingly.
(2) The file "FigS29A-E_thylakoid.pptx" contains representative images for the WT and McG chloroplast, which are used in FigS29A-E.
(3) The file "FigS29F.csv" shows the thylakoid grana number per chloroplast of WT and four McG lines.
Number of variables: 4
Variables:
- genotypes and their chloroplast replicates: 10 of chloroplast replicates of WT and four McG lines are used for calculating the thylakoid grana number per chloroplast
- Numbers: thylakoid grana number in a chloroplast
- AVG: average thylakoid grana number of chloroplast replicates
- SE: standard error of mean of thylakoid grana number
Statistical analysis: Welch's ANOVA test for One-Way-ANOVA test (P-value <0.05). Dunnett's T3 multiple comparisons test for adjusted-P-value.
FigS30 folder:
(1) The file "MetaboAnalyst_R_PCA.R" and " FigS30A_leaf_Conc_PCA.csv" are used to generate the PCA plot (Fig. S30A) for visualizing the difference between the WT and McG leaf lipids.
The FigS30A_leaf_Conc_PCA.csv contains detected lipid concentrations in WT and four McG lines.
Number of variables: 3
Variables:
- metabolite name: lipid name and its chain length
- concentrations (𝜇g g-1FW) of each lipid in leaves
- genotypes and replicates: six biological replicates for WT, McG_2, McG_3, and McG_4 lines. Five replicates for McG_1 line.
(2) The file "HCL.R" is used to generate the "FigS30B_Statistical Analysis_Conc_Heatmap.csv" and the heatmap shown in Fig. S30B.
FigS30B_Statistical Analysis_Conc_Heatmap.csv contains log2-transformed ratio to the WT average of each lipid
Number of variables: 3
Variables:
- genotypes and replicates: six biological replicates for WT, McG_2, McG_3, and McG_4 lines. Five replicates for McG_1 line.
- metabolite name: lipid name and its chain length
- log2-transformed ratio to the WT average of each lipid
(4) The file "FigS30AB_20240305_analysis_PCA_heatmap.ppt" contains the PCA and the heatmap used in FigS30AB.
FigS31 folder:
(1) The file "MetaboAnalyst_R_PCA" and "FigS31A_Seed_Conc_PCA.csv" are used to generate the PCA plot in FigS31A.
The"FigS31A_Seed_Conc_PCA.csv" contains detected lipid concentrations in WT and four McG seeds.
Number of variables: 3
Variables:
- metabolite name: lipid name and its chain length
- concentrations (𝜇g g-1FW) of each lipid in seeds
- genotypes and replicates: six biological replicates for WT, McG_1, McG_2, McG_3, and McG_4 lines.
(2) The file "FigS31B_Statistical Analysis_Seed.csv" and "HCL.R" are used to generate the heatmap in FigS31B.
The file "FigS31B_Statistical Analysis_Seed.csv" contains log2-transformed ratio to the WT average of each lipid in seeds
Number of variables: 3
Variables:
- genotypes and replicates: six biological replicates for WT, McG_1, McG_2, McG_3, and McG_4 line
- metabolite name: lipid name and its chain length
- log2-transformed ratio to the WT average of each lipid
(3) The file "FigS31AB_20240305_analysis_PCA_heatmap.ppt" contain figures transferred from the file "FigS31B_Statistical Analysis_Seed" used for FigS31A-B.
FigS32 folder:
(1) In folder "FigS32A_Leaf_Conc_chainlength", the FigS32A_leaf_Conc.csv and LipidFAD.R are used for generating the .svg files showing concentrations of chain lengths of each lipid shown in Fig.S32A.
The "FigS32A_leaf_Conc.csv" contains detected lipid concentrations (𝜇g g-1FW) in leaves of WT and four McG lines.
Number of variables: 2
Variables:
- metabolite name: lipid name and its chain length
- concentrations (𝜇g g-1FW) of each lipid in leaves
(2) In folder "FigS32B_Seed_Conc_chainlength", "FigS32B_Seed_Conc.csv" and LipidFAD.R are used for generating the .svg files showing concentrations of chain lengths of each lipid shown in Fig.S32B.
The "FigS32B_Seed_Conc.csv" contains detected lipid concentrations (𝜇g g-1FW) in seeds of WT and four McG lines.
Number of variables: 2
Variables:
- metabolite name: lipid name and its chain length
- concentrations (𝜇g g-1FW) of each lipid in seeds.
TableS1_energy cost of CBB MCG.csv:
This file is used for Table S1"Comparison of carbon conversion into acetyl-coA synthesis between the native CBB-PDH pathway and CBB-McG dual-cycle"
Variables:
CBB + PDH: Calvin-Benson-Bassham cycle and pyruvate dehydrogenase pathway
CBB + McG: Calvin-Benson-Bassham cycle with McG cycle
NAD(P)H consumption: number of NADPH molecules is required for one acetyl-coA synthesis.
ATP consumption: number of ATP molecules are required for one acetyl-coA synthesis.
RubisCo turnover per C2: number of RubisCo carboxylation reaction is required for one acetyl-coA synthesis
The theoretical carbon yield per C3: carbon use efficiency of a C3 for an acetyl-coA formation
TableS2_folder:
This folder contains auxin (Indole-3-acetic acid), cytokinin (trans-zeatin), gibberellins (GA), and brassinosteroids (BR) measurements of WT and McG plants. It is used to generate Table S2 "Phytohormone measurements".
(1) "TableS2_BR.csv" file contains BR standard curve and for measuring brassinosteroids (BR) in WT and McG plant leaves.
Number of variables: 6
Variables:
- standard BR concentrations: 50ul solutions of 0, 15.6, 31.25, 62.5, 125, 250, and 500 pmole/L BR
- OD450: absorption at 450nm
- genotypes and their biological replicates: four biological replicates for each genotype
- BR pg g-1FW: concentrations of BR in WT and McG plant leaves
- AVG: average BR concentration of replicates
- SE: standard error of mean of BR concentrations of replicates
(2) "TableS2.csv" file contains GA measurements of WT and McG plant leaves.
Variables:
- standard GA concentrations: 50ul solutions of 0, 15.6, 31.25, 62.5, 125, 250, and 500 pmole/L BR
- OD450: absorption at 450nm
- genotypes and their biological replicates: four biological replicates for each genotype
- GA pg g-1FW: concentrations of GA in WT and McG plant leaves
- AVG: average GA concentration of replicates
- SE: standard error of mean of GA concentrations of replicates
(3)"TableS2_IAA.csv" file contains Indole-3-acetic acid (IAA) measurements of WT and McG plant leaves
Number of Variables:
Variables: 11
- genotype: WT and four McG lines
- bio-rep samples: biological replicates for WT and each line
- tech-rep: 3 technical replicate measurements are performed for each biological replicate
- Area of IAA: detected peak area of IAA in samples
- Area of 13C6-IAA: detected peak area of spiked-in standard13C6-IAA (10ng/10mL extract solution)
- IAA/13C6-IAA ratio: peak area ratio of IAA/13C6-IAA
- mean: mean of peak area ratio of IAA/13C6-IAA of three technical replicates
- 13C6-IAA (ng): concentration of 13C6-IAA in sample extract solution
- FW (g): sample fresh weight (g)
- ng g-1 IAA: concentration of IAA of each sample
- mean: average IAA concentration of 6 biological replicates
(4)"TableS2_trans_Zeatin.csv" file contains Cytokinin (trans-Zeatin) concentrations in WT and McG plant leaves
Number of variables:12
Variables:
- genotype: WT and four McG lines
- bio-rep: 6 biological replicates for WT and each McG line
- tech-rep: 3 technical replicate measurements are performed for each biological replicate
- FW g: fresh weight (g) of each biological replicate
- ml extract bf: milliliter (ml) extraction buffer used for each biological replicate
- ng d5-tz: nanogram (ng) of d5-trans-Zeatin spiked-in ml extract bf
- d5-tZ (s) Area: peak area of spiked in d5-tZ in each sample
- tZ (s) Area: peak area of trans-Zeatin (tZ) in each sample
- tZ (s) ng g-1 FW: concentration of trans-Zeatin (ng g-1 FW) of each sample
- tech replicatesAVG: average tZ concentration of three technical replicate for each biological replicate
- bio replicate AVG: average tZ concentration of six biological replicates
- bio replicate SE: standard error of mean of tZ concentration of six biological replicates
TableS3.csv:
This file contains chlorophyll contents of WT and McG rosette leaves.
Number of variables:14
Variables:
- genotype: WT and four McG lines
- bio-rep: 6 biological replicates
- OD663: absorption at 663nm
- OD646: absorption at 646nm
- OD645:absorption at 645nm
- Chla ug g-1FW: chlorophyll a content of each biological replicate
- Chlb ug g-1FW: chlorophyll b content of each biological replicate
- Total chl ug g-1FW: total chlorophyll content of each biological replicate
- AVG Chla: average chlorophyll a content
- SE Chla: standard error of mean of chlorophyll a content
- AVG Chlb: average chlorophyll b content
- SE Chlb: standard error of mean of chlorophyll b content
- AVG total Chl: average of total chlorophyll content
- SE total Chl: standard error of mean of total chlorophyll content
TableS4 folder
This folder contains measurements for quantify total protein content and carbohydrate contents of the WT and McG leaves.
(1) TableS4_gluc.csv contains glucose contents for WT and McG lines
Number of variables:
Variables: 7
- genotype: WT and four McG lines
- bio-rep: four biological replicates for WT and each line
- FW g: leaf fresh weight (g)
- Glu Area: detected peak area of glucose on HPCL
- STD mM: 10ul of 10-400 mM glucose solution is used for generating standard curve for calculating glucose concentrations in WT and each McG plant samples
- mM in 10ul: Glucose (mM) in 10ul injected sample solution
- mg/g: Glucose content (mg g-1FW)
- AVG: average glucose content of 4 biological replicates
- SE: standard error of mean of glucose content of 4 biological replicates
(2) TableS4_sucrose.csv contains sucrose contents of WT and McG lines
Variables: 7
- genotype: WT and four McG lines
- bio-rep: four biological replicates for WT and each line
- FW g: leaf fresh weight (g)
- Suc Area: detected peak area of sucrose on HPCL
- STD mM: 10ul of 10-400 mM sucrose solution is used for generating standard curve for calculating glucose concentrations in WT and each McG plant samples
- mM in 10ul: Sucrose (mM) in 10ul injected sample solution
- mg/g: Sucrose content (mg g-1FW)
- AVG: average sucrose content of 4 biological replicates
- SE: standard error of mean of sucrose content of 4 biological replicates
(3) TableS4_starch.csv contains starch measurements for WT and McG lines
Variables: 7
- genotype: WT and four McG lines
- bio-rep: four biological replicates for WT and each line
- FW g: leaf fresh weight (g)
- deltaOD340: measured absorbance at 340nm - blank absorbance at 340nm
- mg/g: Starch content (mg g-1FW)
- AVG: average starch content of 4 biological replicates
- SE: standard error of mean of starch content of 4 biological replicates
(4) TableS4_water_soluble_glucan.csv contains soluble glucan measurements for WT and McG lines.
Variables: 7
- genotype: WT and four McG lines
- bio-rep: four biological replicates for WT and each line
- FW g: leaf fresh weight (g)
- deltaOD340: measured absorbance at 340nm - blank absorbance at 340nm
- mg/g: water soluble glucan content (mg g-1FW)
- AVG: average of water soluble glucan content of 4 biological replicates
- SE: standard error of mean of water soluble glucan content of 4 biological replicates
(5) TableS4_protein_BCA.csv file contains protein contents of WT and McG plant leaves.
Variables: 7
- genotype: WT and four McG lines
- bio-rep: four biological replicates for WT and each line
- FW g: leaf fresh weight (g)
- OD562: absorbance at 562nm
- mg/g: protein content (mg) g-1FW
- AVG: average protein content of 4 biological replicates
- SE: standard error of mean of protein content of 4 biological replicates
TableS5.csv:
(1)The file contains concentration of each lipid class in the WT and McG plant leaves.
Number of variables: 6
Variables:
- lipid class: different lipid class
- number: number of lipids in each class
- genotype and replicates: six biological replicates for WT, McG_2, McG_3, and McG_4. Five biological replicates for McG_1
- concentration of lipid shown in each cell: ug g-1FW
- AVG: average lipid content of biological replicates
- SE: standard error of mean of lipid contents of biological replicates
TableS6.csv:
This file contains contents of different lipid classes in WT and McG plant seeds.
Number of variables: 6
Variables:
- lipid class: different lipid class
- number: number of lipids in each class
- genotype and replicates: six biological replicates for WT, McG_1, McG_2, McG_3, and McG_4.
- concentration of lipid shown in each cell: ug g-1FW
- AVG: average lipid content of biological replicates
- SE: standard error of mean of lipid contents of biological replicates
TableS7.csv:
This file contains sequences of the primers and probes for detecting transcriptional levels of McG transgenes in the McG lines.
Number of variables: 5
Variables:
- probe dye: fluorescence dye for measuring expression levels of transgenes (PPC, MTK, MCL, GDH, GCL, TSR) and Arabidopsis endogenous GBSS gene
- Gene name
- Forward: sequence of forward primer
- Probe: sequence of probe
- Reverse: sequence of reverse primer
Code/software
(1) Biorender is used to create Fig. 1.
(2) Geneious Prim is used to analyze whole genome sequence data (.fasta) of the WT and McG lines to identify the insertion sites of the McG transgenes in the genome.
(3) Excel and R Studio are used to analyze raw data and generate figures and tables. The scripts are included in the R files, which are described above.
(4) Prism version 10.4.1 is used for One-way Welch's ANOVA statistical analyses (p-value<0.05) and Dunnett's T3 multiple comparison tests.
Access information
Other publicly accessible locations of the data:
- NA
Data was derived from the following sources:
- NA