Regulatory actors and alternative routes for Arabidopsis seed germination are revealed using a pathway‐based analysis of transcriptomic datasets

Abstract

Summary Regulation of seed germination by dormancy relies on a complex network of transcriptional and post‐transcriptional modifications during seed imbibition that controls seed adaptive responses to environmental cues. High‐throughput technologies have brought significant progress in the understanding of this phenomenon and have led to identify major regulators of seed germination, mostly by studying the behaviour of highly differentially expressed genes. However, the actual models of transcriptome analysis cannot catch additive effects of small variations of gene expression in individual signalling or metabolic pathways, which are also likely to control germination. Therefore, the comprehension of the molecular mechanism regulating germination is still incomplete and to gain knowledge about this process we have developed a pathway‐based analysis of transcriptomic Arabidopsis datasets, to identify regulatory actors of seed germination. The method allowed quantifying the level of deregulation of a wide range of pathways in dormant versus non‐dormant seeds. Clustering pathway deregulation scores of germinating and dormant seed samples permitted the identification of mechanisms involved in seed germination such as RNA transport or vitamin B6 metabolism, for example. Using this method, which was validated by metabolomics analysis, we also demonstrated that Col and Cvi seeds follow different metabolic routes for completing germination, demonstrating the genetic plasticity of this process. We finally provided an extensive basis of analysed transcriptomic datasets that will allow further identification of mechanisms controlling seed germination.

A multiscale approach reveals regulatory players of water stress responses in seeds during germination

“…Initially, we performed a pathway‐based analysis of transcriptomic data using Pathifier, a pipeline that can reveal the involvement of signalling and metabolic pathways in any physiological process (Drier, Sheffer, & Domany, ; Livshits et al, ; Ponnaiah et al, ). The pipeline calculates a score (PDS) representing the extent to which pathways are deregulated in every individual sample, and it quantifies the level of deregulation of a pathway in a sample by measuring the deviation of the sample from the normal behaviour.…”

“…A transcriptomic approach was performed in order to investigate the molecular bases of sunflower seed response to water stress. First, in order to identify pathways that might be associated with water stress tolerance we used Pathifier, a pipeline successfully used for Arabidopsis seed transcriptome analysis (Ponnaiah et al, ). Complementary to the approaches based on differential level of expression of individual genes, Pathifier integrates little variations of gene expression and calculates the deregulation score of a pathway associating several genes (Figure ).…”

“…Analysis has been performed using Pathifier, an algorithm that calculates a pathway deregulation score (PDS) for pathways from gene expression values. It was originally developed to understand pathway deregulation in cancer samples against the normal healthy sample (Drier, Sheffer & Domany, ) and was adapted to Arabidopsis by Ponnaiah et al (). Using values of gene expression, Pathifier provides deregulation scores, which correspond to the extent to which the activity of a pathway in a biological sample differs from the activity of the same pathway estimated in a reference sample.…”

“…We have determined whether seed response to water stress was related to ROS homeostasis and antioxidant enzyme activities, and we performed large‐scale analyses to investigate changes in transcriptome and proteome of these two genotypes in response to water stress. We also have taken advantage of a pipeline recently developed for plants, so‐called Pathifier (Ponnaiah et al, ), to identify metabolic pathways associated with fast germination under water stress from the transcriptomic data. Altogether, our results reveal candidate genes, proteins, and pathways that could play a role in tolerance to water stress during seed germination.…”

Transcriptome and metabolome analyses revealing the potential mechanism of seed germination in Polygonatum cyrtonema

“…Metabolomics has recently become a major research tool to analyze substrates and products in metabolic pathways [6]. Many researches also attempts to developed the variation of gene expression and build comprehensive models of seed germination [7].…”