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.

Keywords: Arabidopsis; curation; leaf anatomy; modelling; organelle.

Graphical abstract

Figure 1.

Arabidopsis leaf 6 anatomy at 21 days after initiation. (a) 3D rendering of reconstructed leaf 6 (21 days after initiation) based on multiphoton laser scanning microscopy data (provided by Nathalie Wuyts). The 3D reconstruction corresponds to a leaf piece located approximately midway between the leaf midvein and margin. (b) Arabidopsis rosette: numbers indicate the true leaf numbers in their order of formation; asterisks indicate cotyledons. See Section 4 for experimental growth conditions. (c–i) Multiphoton laser scanning microscopy images showing the different cell types in the Arabidopsis leaf in the (x,y) plane, as indicated in the pictures (adaptation from original data provided by N. Wuyts). (c,g) Abaxial (bottom) and adaxial (top) epidermis, respectively, with epidermal pavement cells and stomata complexes. (f) SEM image showing a trichome cell and its basal cells (image courtesy of Michèle Crèvecoeur). (h,i) Longitudinal section of a minor vein with phloem and xylem, respectively. Numbers in (c–i) refer to cell types (in alphabetical order): 1, abaxial (bottom) epidermal pavement cells; 2, adaxial (top) epidermal pavement cells; 3, basal trichome cells; 4, bundle sheath cells; 5, palisade mesophyll cells; 6, phloem companion cells; 7, phloem parenchyma (transfer) cells; 8, phloem sieve elements; 9, spongy mesophyll cells; 10, stomata cells; 11, trichome cells; 12, xylem parenchyma cells; 13, xylem tracheids. Cambial vein cells and hydathode cells are not displayed here.

Figure 2.

Graphical representation of the cellular and subcellular metrics of leaf 6. (a) Cell numbers; (b) volume occupancy in Arabidopsis reference leaf 6 in μL/g LFW. Growth conditions are 21 DAI, 16H light, 166 μmol photons m^-2 s^-1, 20.5°C, relative humidity 72%. See Table 2 for further details. (c) Relative subcellular volumes in an Arabidopsis reference leaf 6 in μL/g LFW. As data were incomplete for the other cell types (see Supplementary Table S2), the leaf was simplified as an assemblage of mesophyll cells and epidermal pavement cells (representing 94% of the leaf volume; see Table 3.). Figure generated using Flourish (https://flourish.studio/).