RT Journal Article
SR Electronic
T1 The annotation and analysis of complex 3D plant organs using 3DCoordX
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.11.20.469364
DO 10.1101/2021.11.20.469364
A1 Vijayan, Athul
A1 Strauss, Soeren
A1 Tofanelli, Rachele
A1 Mody, Tejasvinee Atul
A1 Lee, Karen
A1 Tsiantis, Miltos
A1 Smith, Richard S.
A1 Schneitz, Kay
YR 2021
UL http://biorxiv.org/content/early/2021/11/20/2021.11.20.469364.abstract
AB 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.Competing Interest StatementThe authors have declared no competing interest.