Computational Tools for Serial Block Electron Microscopy Reveal Plasmodesmata Distributions and Wall Environments.

Abstract

Plasmodesmata are small channels that connect plant cells. While recent technological advances have facilitated analysis of the ultrastructure of these channels, there are limitations to efficiently addressing their presence over an entire cellular interface. Here, we highlight the value of serial block electron microscopy for this purpose. We developed a computational pipeline to study plasmodesmata distributions and detect the presence/absence of plasmodesmata clusters, or pit fields, at the phloem unloading interfaces of Arabidopsis ( Arabidopsis thaliana ) roots. Pit fields were visualized and quantified. As the wall environment of plasmodesmata is highly specialized, we also designed a tool to extract the thickness of the extracellular matrix at and outside of plasmodesmata positions. We detected and quantified clear wall thinning around plasmodesmata with differences between genotypes, including the recently published plm-2 sphingolipid mutant. Our tools open avenues for quantitative approaches in the analysis of symplastic trafficking.

Code and data availability

The paper's authors publicly released their Matlab plugins for plasmodesmata distribution and cell-wall thickness analysis on GitHub, a guided R analysis pipeline tutorial, and the Col-0 SB-EM data sets with segmented wall models and PD annotations on Figshare. Generic tools (MIB, matGeom, CRAN packages) and the EMPIAR