Data from: Integrative analysis of CAM photosynthesis reveals its impact on primary metabolism inYucca
Data files
Jun 08, 2026 version files 107.95 MB
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FICUS_soil_moisture_2021.csv
5.13 KB
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LICORdata_static.csv
135.79 KB
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README.md
13.28 KB
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YA_metab_count.csv
171.82 KB
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YA_metab_design.csv
2.49 KB
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YA_mRNA_design.csv
1.66 KB
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YA_mRNA_TPM.csv
42.36 MB
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YA_prot_count.csv
8.33 MB
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YA_prot_design.csv
1.83 KB
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YA_TA.csv
1.33 KB
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YF_metab_count.csv
152.64 KB
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YF_metab_design.csv
2.85 KB
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YF_mRNA_design.csv
1.68 KB
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YF_mRNA_TPM.csv
47.76 MB
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YF_prot_count.csv
9.02 MB
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YF_prot_design.csv
1.83 KB
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YF_TA.csv
602 B
Abstract
Crassulacean Acid Metabolism (CAM) is an adaptation that temporally separates carbon uptake at night from photosynthesis during the day. CAM has evolved repeatedly across vascular plants, perhaps, in part, because it does not involve any novel gene functions and instead relies on regulatory modification of existing C3pathways. The co-option of established processes and corresponding alteration of metabolic flux is likely to impact other primary metabolic pathways such as nitrogen metabolism and photorespiration. However, the majority of CAM research to date has focused on a handful of genes in the core CAM pathway. Understanding the complex downstream effects associated with the emergence of CAM is essential to explaining its convergent evolution as well as efforts to engineer carbon concentrating mechanisms in crops. In this study, we integrate genomic, transcriptomic, proteomic, and metabolomic data to compare primary metabolism between the CAM species Yucca aloifolia and closely related C3species, Y. filamentosa. Despite substantial differences in metabolite abundance across multiple pathways, including citrate and nitrogen metabolism, we observe relatively few gene expression differences outside of the core CAM pathway. Additionally, we observe minimal correlation between protein abundance and mRNA expression, suggesting significant post-transcriptional regulation in CAM species. Our findings provide insights into the metabolic shifts associated with CAM evolution and highlight the complexity of its regulation at multiple biological levels.
Dataset DOI: 10.5061/dryad.5mkkwh7ft
Corresponding author / contact
Name: David Wickell
Institution: University of Connecticut
Email: david.wickell@uconn.edu
Related manuscript / preprint
- BioRxiv (methods + study context): https://www.biorxiv.org/content/10.1101/2024.11.01.621533v2.full
Dataset overview
This repository contains physiological and multi-omics data collected in 2021 at the University of Georgia from two Yucca species (Yucca aloifolia and Yucca filamentosa) under contrasting water availability treatments and sampled across a diel time course. Physiological measurements (gas exchange, titratable acidity, soil moisture/environmental monitoring) were collected alongside leaf tissue for metabolomic, proteomic, and transcriptomic profiling. Data include metabolomics, proteomics, transcriptomics, and physiology, along with design files describing sample metadata (treatment, sampling time, replicate/genotype identifiers).
Dates of data collection
- Experiments and sampling: 2021
File descriptions (brief)
Metabolomics
- YA_metab_count.csv — metabolite abundance table for Y. aloifolia
- YA_metab_design.csv — sample metadata for Y. aloifolia metabolomics
- YF_metab_count.csv — metabolite abundance table for Y. filamentosa
- YF_metab_design.csv — sample metadata for Y. filamentosa metabolomics
Transcriptomics
- YA_mRNA_TPM.csv — transcript expression (TPM) for Y. aloifolia
- YA_mRNA_design.csv — sample metadata for Y. aloifolia transcriptomics
- YF_mRNA_TPM.csv — transcript expression (TPM) for Y. filamentosa
- YF_mRNA_design.csv — sample metadata for Y. filamentosa transcriptomics
Proteomics
- YA_prot_count.csv — protein abundance table for Y. aloifolia
- YA_prot_design.csv — sample metadata for Y. aloifolia proteomics
- YF_prot_count.csv — protein abundance table for Y. filamentosa
- YF_prot_design.csv — sample metadata for Y. filamentosa proteomics
Physiology
- LICORdata_static.csv — gas exchange (LI-COR) output data (static measurements)
- YA_TA.csv — titratable acidity data for Y. aloifolia
- YF_TA.csv — titratable acidity data for Y. filamentosa
- FICUS_soil_moisture_2021.csv — soil moisture / environmental monitoring for 2021
License
This dataset is made available under the CC0 1.0 Universal (CC0 1.0) Public Domain Dedication.
Funding
A portion of this research was performed under the Facilities Integrating Collaborations for User Science (FICUS) program (proposal:10.46936/fics.proj.2020.51552/60000215) and used resources at the DOE Joint Genome Institute (https://ror.org/04xm1d337) and the Environmental Molecular Sciences Laboratory (https://ror.org/04rc0xn13), which are DOE Office of Science User Facilities operated under Contract Nos. DE-AC02-05CH11231 (JGI) and DE-AC05-76RL01830 (EMSL).
Files and variables (detailed)
File: YA_metab_design.csv
Description:
Sample metadata for metabolomic profiling of Yucca aloifolia. This file links each metabolomics sample to its experimental condition, diel sampling time, and biological replicate.
Variables:
- Sample names: Unique sample identifiers corresponding to column names in
YA_metab_count.csv - Condition: Watering treatment applied to the plant at the time of sampling
- Condition1 = well-watered
- Condition2 = drought
- Time point: Diel sampling time (zeitgeber time, hours)
- Replicate/Individual: Biological replicate or individual plant identifier
File: YF_metab_design.csv
Description:
Sample metadata for metabolomic profiling of Yucca filamentosa. This file links each metabolomics sample to its experimental condition, diel sampling time, and biological replicate.
Variables:
- Sample names: Unique sample identifiers corresponding to column names in
YF_metab_count.csv - Condition: Watering treatment applied to the plant at the time of sampling
- Condition1 = well-watered
- Condition2 = drought
- Time point: Diel sampling time (zeitgeber time, hours)
- Replicate/Individual: Biological replicate or individual plant identifier
File: FICUS_soil_moisture_2021.csv
Description:
Soil moisture measurements collected during the 2021 experiment to track changes in volumetric water content following withholding of water. Measurements are reported for individual plants of both Yucca aloifolia and Yucca filamentosa across multiple days. NA values represent missing measurements.
Variables:
- sample: Biological replicate identifier
- species: Species name (Y_aloifolia or Y_filamentosa)
- day_since_withholding: Number of days since water was withheld
- date: Calendar date of measurement (MM/DD/YY)
- percent_moisture: Volumetric soil moisture percentage
File: LICORdata_static.csv
Description:
Gas exchange measurements collected using a LI-COR photosynthesis system. Data include photosynthetic rate, stomatal conductance, transpiration, intercellular CO₂ concentration, environmental conditions, and instrument diagnostics.
Variables:
(Variables follow LI-COR standard output naming conventions.)
- species: Species identity
- genotype: Individual or genotype identifier
- treat: Watering treatment
- zt: Zeitgeber time (hr)
- Obs: Observation number
- HHMMSS: Time of measurement (hr:m:s)
- FTime: Flow time (s)
- EBal?: Energy balance flag
- 0 = Energy balance solution converged normally (good).
- 1 = Energy balance calculation failed or did not converge.
- Photo: Net photosynthetic rate (μmol CO₂ m⁻² s⁻¹)
- Cond: Stomatal conductance (mol H₂O m⁻² s⁻¹)
- Ci: Intercellular CO₂ concentration (μmol mol⁻¹ (ppm))
- Trmmol: Transpiration rate (mmol H₂O m⁻² s⁻¹)
- VpdL: Leaf vapor pressure deficit (kPa)
- CTleaf: Leaf temperature (°C)
- Area: Leaf area (cm²)
- BLC_1: One-sided boundary layer conductance (mol H₂O m⁻² s⁻¹)
- StmRat: Stomatal ratio = fraction of stomata on the upper vs. lower leaf surface
- BLCond: Total boundary layer conductance (mol H₂O m⁻² s⁻¹)
- Tair, Tleaf, TBlk: Air, leaf, and block temperatures, respectively (°C)
- CO2R: Reference CO₂ (μmol mol⁻¹ (ppm))
- CO2S: Sample CO₂ (μmol mol⁻¹ (ppm))
- H2OR: Reference H₂O (mmol mol⁻¹)
- H2OS: Sample H₂O (mmol mol⁻¹)
- RH_R: Reference relative humidity (%)
- RH_S: Sample relative humidity (%)
- Flow: Flow rate (μmol s⁻¹)
- PARi: Outgoing Photosynthetically Active Radiation (μmol photons m⁻² s⁻¹)
- PARo: Incident Photosynthetically Active Radiation (μmol photons m⁻² s⁻¹)
- Press: Atmospheric pressure (kPa)
- (Remaining variables - not typically used for analysis):
Derived gas-exchange statistics, quality metrics, and instrument diagnostics as defined by LI-COR software. Detailed explanations of each variable can be found in the LI-6800 operating instructions: https://www.licor.com/support/LI-6800/topics/symbols.html
File: YA_TA.csv
Description:
Titratable acidity measurements for Yucca aloifolia collected across a diel cycle and treatments. NA values represent missing measurements.
Variables:
- Genotype: Individual plant identifier
- Time: Sampling time point
- Treatment: Watering treatment
- Condition1 = well-watered
- Condition2 = drought
- Weight_g: Fresh tissue mass (g)
- pH_start: Initial extract pH
- ul_pH6.5: Volume of NaOH to pH 6.5
- ul_pH7.0: Volume of NaOH to pH 7.0
- Total_ul: Total NaOH volume added
- ul_per_mg: Volume normalized by tissue mass
- umol_NaOH_per_mg: Acid content per mg tissue
- umol_NaOH_per_g: Acid content per g tissue
File: YF_TA.csv
Description:
Titratable acidity measurements for Yucca filamentosa collected across a diel cycle and treatments.
Variables:
- Genotype: Individual plant identifier
- Time: Sampling time point
- Treatment: Watering treatment
- Condition1 = well-watered
- Condition2 = drought
- Weight_g: Fresh tissue mass (g)
- pH_start: Initial extract pH
- ul_pH6.5: Volume of NaOH to pH 6.5
- ul_pH7.0: Volume of NaOH to pH 7.0
- Total_ul: Total NaOH volume added
File: YA_metab_count.csv
Description:
Metabolite abundance table for Yucca aloifolia. Rows correspond to metabolites and columns correspond to individual samples spanning treatments and diel time points.
Variables:
- Metabolite: Metabolite identifier or name
- Hey_Ya columns: Metabolite abundance values for individual samples. Sample names encode species (Ya), treatment (D = drought, W = well-watered), time point, individual, and replicate. Exact sample metadata are provided in
YA_metab_design.csv
File: YF_metab_count.csv
Description:
Metabolite abundance table for Yucca filamentosa. Rows correspond to metabolites and columns correspond to individual samples spanning treatments and diel time points.
Variables:
- Metabolite: Metabolite identifier or name
- Hey_Yf columns: Metabolite abundance values for individual samples. Sample names encode species (Yf), treatment, time point, individual, and replicate. Sample metadata are provided in
YF_metab_design.csv
File: YA_prot_count.csv
Description:
Protein abundance table for Yucca aloifolia derived from proteomic analyses. Blank values indicate samples in which the protein was not detected.
Variables:
- Protein: Protein identifier
- Description: Functional annotation or description
- Mass: Protein molecular mass
- SeqLen: Protein sequence length
- Unique_Peptide_Count: Number of unique peptides detected
- Unique_Clean_Sequence_Count: Number of unique high-confidence peptide sequences
- Rep_W / Rep_D columns: Protein abundance values for individual samples under well-watered (W) or drought (D) treatments. Sample metadata are provided in
YA_prot_design.csv
File: YF_prot_count.csv
Description:
Protein abundance table for Yucca filamentosa derived from proteomic analyses. Blank values indicate samples in which the protein was not detected.
Variables:
Same structure and definitions as YA_prot_count.csv, with abundance columns corresponding to Y. filamentosa samples. Sample metadata are provided in YF_prot_design.csv.
File: YA_mRNA_design.csv
Description:
Sample metadata for transcriptomic profiling of Yucca aloifolia.
Variables:
- Sample name: Sample identifier matching columns in
YA_mRNA_TPM.csv - Condition: Watering treatment
- Time point: Diel sampling time
- Replicate: Biological replicate identifier
File: YF_mRNA_design.csv
Description:
Sample metadata for transcriptomic profiling of Yucca filamentosa.
Variables:
- Sample name: Sample identifier matching columns in
YF_mRNA_TPM.csv - Condition: Watering treatment
- Time point: Diel sampling time
- Replicate: Biological replicate identifier
File: YA_mRNA_TPM.csv
Description:
Transcript abundance (TPM) table for Yucca aloifolia.
Variables:
- geneIDs: Gene identifiers
- Rep_W / Rep_D columns:
TPM values for individual samples under well-watered (W) or drought (D) treatments.
File: YF_mRNA_TPM.csv
Description:
Transcript abundance (TPM) table for Yucca filamentosa.
Variables:
- geneIDs: Gene identifiers
- Rep_W / Rep_D columns:
TPM values for individual samples under well-watered (W) or drought (D) treatments.
File: YA_prot_design.csv
Description:
Sample metadata for proteomic profiling of Yucca aloifolia.
Variables:
- Sample: Sample identifier
- Condition: Watering treatment
- Condition1 = well-watered
- Condition2 = drought
- Time Point: Diel sampling time
- Replicate: Biological replicate identifier
File: YF_prot_design.csv
Description:
Sample metadata for proteomic profiling of Yucca filamentosa.
Variables:
- Sample: Sample identifier
- Condition: Watering treatment
- Condition1 = well-watered
- Condition2 = drought
- Time point: Diel sampling time
- Replicate: Biological replicate identifier
Access information
Other publicly accessible locations of the data:
- RNA seq data for gene expression profiling analyses can be found in NCBI’s Sequencing Read Archive; SRA BioProject numbers: 'PRJNA1162856', 'PRJNA1162850', 'PRJNA1162828', 'PRJNA1162846', 'PRJNA1162829', 'PRJNA1162847', 'PRJNA1162862', 'PRJNA1162861', 'PRJNA1162852', 'PRJNA1162845', 'PRJNA1162853', 'PRJNA1162857'.