Gene expression analysis of Cyanophora paradoxa reveals conserved abiotic stress responses between basal algae and flowering plants

Abstract

The glaucophyte Cyanophora paradoxa represents the most basal member of the kingdom Archaeplastida, but the function and expression of most of its genes are unknown. This information is needed to uncover how functional gene modules, that is groups of genes performing a given function, evolved in the plant kingdom.We have generated a gene expression atlas capturing responses of Cyanophora to various abiotic stresses. The data were included in the CoNekT-Plants database, enabling comparative transcriptomic analyses across two algae and six land plants.We demonstrate how the database can be used to study gene expression, co-expression networks and gene function in Cyanophora, and how conserved transcriptional programs can be identified. We identified gene modules involved in phycobilisome biosynthesis, response to high light and cell division. While we observed no correlation between the number of differentially expressed genes and the impact on growth of Cyanophora, we found that the response to stress involves a conserved, kingdom-wide transcriptional reprogramming, which is activated upon most stresses in algae and land plants.The Cyanophora stress gene expression atlas and the tools found in the https://conekt.pla nt.tools/ database thus provide a useful resource to reveal functionally related genes and stress responses in the plant kingdom.

Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses

“…Since younger gene families show a higher degree of organ-specific gene expression 40 , we speculated that younger gene families could have evolved to provide adaptations to specialized environments and their abiotic stresses. However, we observed similar stress responsiveness patterns for the oldest gene families (Archaeplastida, Figure 3B, red line) and the much younger Marchantiaspecific gene families (Mpo, green line), suggesting that younger gene families are not more active in stress responses, which is in line with our previous observation in Cyanophora 20 .…”

“…Plants have evolved sophisticated mechanisms to perceive and respond to the different stresses, which induces an acclimation process that allows the plant to survive the stress 18 , but often at the cost of reduced growth 16,17 . Many studies have analysed the effect of stress on plant growth by identifying differentially expressed genes between stress-treated and untreated plants (e.g., [19][20][21] ), or by identifying single nucleotide polymorphisms associated with stress resistance in Arabidopsis and maize [22][23][24] . The studies performed on non-agricultural species such as Arabidopsis can shed light on fundamental processes of stress acclimation, but it is currently unclear whether the acclimation mechanisms between different species or even accessions are conserved and transferable from model to crop.…”

LSTrAP-Kingdom: an automated pipeline to generate annotated gene expression atlases for kingdoms of life

“…Furthermore, when combined with genomic information, comparative transcriptomic analyses across species allow the study of the function and evolution of genes from the perspective of gene expression (Ferrari et al, 2019;Wen Tan and Mutwil, 2019;Ferrari et al, 2020;Ng et al, 2019;Ferrari and Mutwil, 2019;Lim et al, 2020).…”

LSTrAP-Kingdom: an automated pipeline to generate annotated gene expression atlases for kingdoms of life

“…Furthermore, when combined with genomic information, comparative transcriptomic analyses across species allow the study of the function and evolution of genes from the perspective of gene expression (Ferrari et al, 2019;Wen Tan and Mutwil, 2019;Ferrari et al, 2020;Ng et al, 2019;Ferrari and Mutwil, 2019;Lim et al, 2020).…”