AUTOMATIC EXTRACTION OF ACTIN NETWORKS IN PLANTS

Abstract

A bstract The actin cytoskeleton is essential in eukaryotes, not least in the plant kingdom where it plays key roles in cell expansion, cell division, environmental responses and pathogen defence. Yet, the precise structure-function relationships of properties of the actin network in plants are still to be unravelled, including details of how the network configuration depends upon cell type, tissue type and developmental stage. Part of the problem lies in the difficulty of extracting high-quality, three-dimensional, quantitative measures of actin network features from microscopy data. To address this problem, we have developed DRAGoN, a novel image analysis algorithm that can automatically extract the actin network across a range of cell types, providing seventeen different quantitative measures that describe the network at a local level. Using this algorithm, we then studied a number of cases in Arabidopsis thaliana , including several different tissues, a variety of actin-affected mutants, and cells responding to powdery mildew. In many cases we found statistically-significant differences in actin network properties. In addition to these results, our algorithm is designed to be easily adaptable to other tissues, mutants and plants, and so will be a valuable asset for the study and future biological engineering of the actin cytoskeleton in globally-important crops.

Plant phenotyping relevance

植物の顕微鏡画像からアクチンネットワークの構造特性を自動抽出する画像解析手法を開発しており、植物状態の定量的表現型取得が中心である。

Code and data availability

The paper's DRAGoN actin-network extraction algorithm (authors' analysis code) is explicitly stated to be freely available and open source on GitHub. No public phenotype dataset or image deposit is described in the supplied blocks.