Integration of Cross Species RNA-seq Meta-Analysis and Machine-Learning Models Identifies the Most Important Salt Stress-Responsive Pathways in Microalga Dunaliella

Abstract

Photosynthetic microalgae are potentially yielding sources of different high-value secondary metabolites. Salinity is a complex stress that influences various metabolite-related pathways in microalgae. To obtain a clear view of the underlying metabolic pathways and resolve contradictory information concerning the transcriptional regulation of Dunaliella species in salt stress conditions, RNA-seq meta-analysis along with systems levels analysis was conducted. A p-value combination technique with Fisher method was used for cross species meta-analysis on the transcriptomes of two Dunaliella salina and Dunaliella tertiolecta species. The potential functional impacts of core meta-genes were surveyed based on gene ontology and network analysis. In the current study, the integration of supervised machine-learning algorithms with RNA-seq meta-analysis was performed. The analysis shows that the lipid and nitrogen metabolism, structural proteins of photosynthesis apparatus, chaperone-mediated autophagy, and ROS-related genes are the keys and core elements of the Dunaliella salt stress response system. Cross-talk between Ca²⁺ signal transduction, lipid accumulation, and ROS signaling network in salt stress conditions are also proposed. Our novel approach opens new avenues for better understanding of microalgae stress response mechanisms and for selection of candidate gene targets for metabolite production in microalgae.

Keywords: Dunaliella; RNA-seq meta-analysis; ROS; machine learning; network; retrograde signaling; tetrapyrrole.

Figure 1

Metabolic overview of differentially expressed genes of D. tertiolecta (PRJNA51835) in responses to salt stress.

Figure 2

Venn diagram of identified meta-genes in three data sets based on Fisher method.

Figure 3

Clustering of metagenes based on expression patterns in three data sets. The fold changes were used as the expression value in constructing heatmap.

Figure 4

Protein–protein interaction network of meta-genes. The unconnected meta-genes were removed from constructed network. Meta-genes were signed by red circles.