The annotation and analysis of complex 3D plant organs using 3DCoordX

Abstract

A fundamental question in biology concerns how molecular and cellular processes become integrated during morphogenesis. In plants, characterization of 3D digital representations of organs at single-cell resolution represents a promising approach to addressing this problem. A major challenge is to provide organ-centric spatial context to cells of an organ. We developed several general rules for the annotation of cell position and embodied them in 3DCoordX, a user-interactive computer toolbox implemented in the open-source software MorphoGraphX. It enables rapid spatial annotation of cells even in highly curved biological shapes. With the help of 3DCoordX we obtained new insight by analyzing cellular growth patterns in organs of several species. For example, the data indicated the presence of a basal cell proliferation zone in the ovule primordium of Arabidopsis thaliana. Proof-of-concept analyses suggested a preferential increase in cell length associated with neck elongation in the archegonium of Marchantia polymorpha and variations in cell volume linked to central morphogenetic features of a trap of the carnivorous plant Utricularia gibba. Our work demonstrates the broad applicability of the developed strategies as they provide organ-centric spatial context to cellular features in plant organs of diverse shape complexity.

A future in 3D: Analyzing morphology in all dimensions

“…In this issue, Vijayan et al (2022) present a tool for the automatic characterization and analysis of plant tissue morphology. By incorporating information on the organ axis and extracting the cells in different tissue layers based on the organ surface, the authors were able to automatically annotate cellular layers of even complex morphology; exemplified by ovule and funiculus (ovule stalk) development in Arabidopsis ( Arabidopsis thaliana ), the archegonium (female reproductive structure) of the model species the common liverwort ( Marchantia polymopha ), and the cup-shaped trap of the aquatic carnivorous plant the floating bladderwort ( Utricularia gibba ).…”

“… Schematic overview of tissue and cell layer annotation accounting for the growth axis as implemented by Vijayan et al (2022) A, straight tissue structure and B, curved tissue structure. In straight tissues, the distance from a reference point (dashed line) remains constant for each cell layer (i.e.…”