The Arabidopsis leaf quantitative atlas: a cellular and subcellular mapping through unified data integration

Abstract

Quantitative analyses and models are required to connect a plant’s cellular organisation with its metabolism. However, quantitative data are often scattered over multiple studies, and finding such data and converting them into useful information is time-consuming. Consequently, there is a need to centralise the available data and to highlight the remaining knowledge gaps. Here, we present a step-by-step approach to manually extract quantitative data from various information sources, and to unify the data format. First, data from Arabidopsis leaf were collated, checked for consistency and correctness and curated by cross-checking sources. Second, quantitative data were combined by applying calculation rules. They were then integrated into a unique comprehensive, referenced, modifiable and reusable data compendium representing an Arabidopsis reference leaf. This atlas contains the metrics of the 15 cell types found in leaves at the cellular and subcellular levels.

Anatomics MLT, an AI tool for large scale quantification of ultrastructural traits

“…The quantification of anatomical traits is of fundamental importance for recent efforts in crop improvement and the generation of cell– and tissue atlases (Lee et al ., 2023; Tolleter et al ., 2024). Anatomics MLT will provide a useful tool for gathering large-scale input data.…”

Single-cell proteomics of Arabidopsis leaf mesophyll identifies drought stress-related proteins

“…As mesophyll cells do not appear to have unique cell type markers 44 , we relied on the observation that they instead are enriched for proteins involved in photosynthesis (LHCs) and carbon fixation (RuBisCo). Indeed, it has been demonstrated that the fractional volume occupancy of chloroplasts in mesophylls is much higher (9.3% for mesophyll palisade and 15.5% for spongy mesophyll) than epidermal cells (0.45% for abaxial and 0.22% for adaxial) 45 . In agreement with the high-volume chloroplast occupancy in the mesophyll cell type, we observe LHC and RuBisCo proteins represent up to 46% of protein copies on average in well-watered protoplasts in this study.…”