ReadMe File For Experimental datasets underpinning: Manipulation of Chloroplast Development to Enhance Photosynthesis and Nutritional Value of Tomato Dataset DOI: https://doi.org/10.5258/SOTON/D3875 ReadMe Author: Erick Ramon Gomes Oliveira, University of Southampton ORCID ID: 0000-0002-1543-9660 This dataset supports the thesis entitled: Manipulation of Chloroplast Development to Enhance Photosynthesis and Nutritional Value of Tomato AWARDED BY: University of Southampton DATE OF AWARD: 2026 Date of data collection: 2021–2025 Information about geographic location of data collection: University of Southampton, School of Biological Sciences, Southampton, United Kingdom. Additional experimental work was conducted at NIAB East Malling and the University of Essex. Licence: Creative Commons Attribution (CC-BY 4.0) Related projects/Funders: SoCoBio Doctoral Training Partnership -------------------- DATA & FILE OVERVIEW -------------------- This dataset contains experimental measurements generated during the investigation of chloroplast development and photosynthetic performance in transgenic tomato (Solanum lycopersicum cv. Micro-Tom) lines engineered to alter chloroplast development and division. The dataset includes measurements from transgenic lines expressing genes associated with chloroplast development and division, including BpMADS, AtCGA1, and the chloroplast division double construct AtPDV1/PDV2. Files included in the dataset: ACI-Gas_exchange.xlsx Gas exchange measurements derived from A/Ci response curves used to analyse photosynthetic carbon assimilation parameters in tomato fruit tissues. AQ-Gas_exchange.xlsx Photosynthetic gas exchange measurements obtained under varying light conditions for transgenic and control tomato lines. Light_response.csv Light response curve measurements used to determine photosynthetic performance under increasing irradiance. Microscopy.csv Quantification data derived from microscopy analyses of tomato fruit pericarp tissues, including measurements related to chloroplast coverage and density in wild-type and transgenic lines. Pigments Green.xlsx Quantification of chlorophyll and carotenoid content in mature green tomato fruits from wild-type and transgenic lines. Pigments Ripe.xlsx Quantification of carotenoid pigments including lycopene and beta-carotene in ripe tomato fruits. Relationship between files, if important for context: These datasets correspond to experimental measurements described in the associated PhD thesis and support analyses of pigment accumulation, chloroplast morphology, and photosynthetic performance in genetically engineered tomato lines. Additional related data collected that was not included in the current data package: Additional experimental observations, intermediate analyses, and raw instrument outputs associated with some experiments described in the thesis are not included in this dataset. If data was derived from another source, list source: All data were generated as part of the doctoral research project. If there are multiple versions of the dataset: Not applicable. -------------------------- METHODOLOGICAL INFORMATION -------------------------- Description of methods used for collection/generation of data: Tomato (Solanum lycopersicum cv. Micro-Tom) plants were genetically transformed to overexpress genes involved in chloroplast development and division, including BpMADS, AtCGA1, and the chloroplast division double construct AtPDV1/PDV2. Transgenic plants were grown under controlled conditions and fruit tissues were analysed at different developmental stages. Experimental measurements included pigment quantification, chlorophyll fluorescence measurements, gas exchange analysis, and microscopy analysis of chloroplast morphology. Detailed experimental procedures are described in the associated PhD thesis. Methods for processing the data: Raw instrument outputs were exported and compiled using spreadsheet software and processed for statistical analysis and visualisation. Software- or Instrument-specific information needed to interpret the data: Datasets can be opened using Microsoft Excel or compatible spreadsheet software. Data processing and statistical analyses were performed using R (RStudio environment). Microscopy image analysis and quantification were conducted using Fiji (ImageJ). Standards and calibration information, if appropriate: Instrumentation used for chlorophyll fluorescence and gas exchange measurements was calibrated according to manufacturer specifications prior to measurements. Environmental/experimental conditions: Tomato plants were grown under controlled environmental conditions and analysed at specific fruit developmental stages. Describe any quality-assurance procedures performed on the data: Measurements were conducted using biological replicates and analysed statistically to ensure reliability and reproducibility of results. People involved with sample collection, processing, analysis and/or submission: Erick Ramon Gomes Oliveira – experimental design, data collection, analysis and dataset preparation Supervisors: Dr Andrew Simkin, Professor Matthew Terry -------------------------- DATA-SPECIFIC INFORMATION -------------------------- Number of variables: Varies depending on the dataset file. Number of cases/rows: Varies depending on the experimental dataset. Variable list: Common variables include photosynthetic parameters such as Fv/Fm (maximum quantum yield of photosystem II), ΦPSII (effective quantum yield of photosystem II), and ETR (electron transport rate), as well as pigment concentration measurements. Missing data codes: Missing values are represented as blank cells where applicable. Specialized formats or other abbreviations used: Standard abbreviations for photosynthetic parameters and pigment measurements are used. Date that the file was created: March 2026