Global transcriptome analysis identifies critical functional modules associated with multiple abiotic stress...

Area of Science:

• * Algal biotechnology
• * Systems biology
• * Plant stress responses

Background:

• * Understanding stress responses in algae is crucial for optimizing metabolite production.
• * Chromochloris zofingiensis is a model organism for studying algal stress adaptation.

Purpose of the Study:

• * To elucidate the regulatory mechanisms of Chromochloris zofingiensis under stress conditions using a systems biology approach.
• * To identify key gene co-expression modules and transcription factors involved in stress response.

Main Methods:

• * Meta-analysis of gene expression data using p-value combination.
• * Construction and preservation analysis of weighted gene co-expression networks (WGCNA).
• * Inference of gene regulatory networks (GRNs) using ensemble of trees algorithm.

Main Results:

• * Identified 12 co-expression modules, with six showing altered connectivity under stress (non-preserved modules).
• * Enriched pathways in non-preserved modules include Oxidative phosphorylation, Vitamin B6 metabolism, and Arachidonic acid metabolism.
• * Discovered specific transcription factors (e.g., C3H, SBP) regulating key hub genes (e.g., Cz06g10250, Cz03g12130) in stress-responsive networks.

Conclusions:

• * The study reveals significant shifts in gene co-expression and regulatory networks in C. zofingiensis under stress.
• * Identified specific transcription factors and pathways provide targets for enhancing stress tolerance and metabolite production.