Key Pathways and Genes of Arabidopsis thaliana and Arabidopsis halleri Roots under Cadmium Stress Responses: Differences and Similarities

Abstract

Cadmium (Cd) is among the world’s major health concerns, as it renders soils unsuitable and unsafe for food and feed production. Phytoremediation has the potential to remediate Cd-polluted soils, but efforts are still needed to develop a deep understanding of the processes underlying it. In this study, we performed a comprehensive analysis of the root response to Cd stress in A. thaliana, which can phytostabilize Cd, and in A. halleri, which is a Cd hyperaccumulator. Suitable RNA-seq data were analyzed by WGCNA to identify modules of co-expressed genes specifically associated with Cd presence. The results evidenced that the genes of the hyperaccumulator A. halleri mostly associated with the Cd presence are finely regulated (up- and downregulated) and related to a general response to chemical and other stimuli. Additionally, in the case of A. thaliana, which can phytostabilize metals, the genes upregulated during Cd stress are related to a general response to chemical and other stimuli, while downregulated genes are associated with functions which, affecting root growth and development, determine a deep modification of the organ both at the cellular and physiological levels. Furthermore, key genes of the Cd-associated modules were identified and confirmed by differentially expressed gene (DEG) detection and external knowledge. Together, key functions and genes shed light on differences and similarities among the strategies that the plants use to cope with Cd and may be considered as possible targets for future research.

Water deficit response in nodulated soybean roots: a comprehensive transcriptome and translatome network analysis

“…Notably, the biological processes represented in these modules were translation, DNA replication, regulation of transcription, protein ubiquitination, nodulation, and protein phosphorylation (Figure S2 ). This evidences once again the association between the DEGs’ enriched modules and the plant response mechanisms under evaluation and also that performing the differential expression analysis in the functional context of WGCNA facilitates the interpretation of complex scenarios as in the current study [ 39 , 40 ]. Likewise, this strategy was proper when we analyzed the DEGs common to comparisons i and iii and to ii and iv , i.e., the DEGs common to the plants’ responses to water deficit and nodulation, respectively (Table S6 , Table S7 ).…”