Root and shoot biology of Arabidopsis halleri dissected by WGCNA: an insight into the organ pivotal pathways and genes of an hyperaccumulator

Hassan, Sayyeda Hira; Sferra, Gabriella; Simiele, Melissa; Scippa, Gabriella Stefania; Morabito, Domenico; Trupiano, Dalila

doi:10.1007/s10142-022-00897-x

Cited by 3 publications

(8 citation statements)

References 92 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…RNA‐seq analysis showed that upregulated DEGs were enriched in the photosynthesis pathway (Figure 7; Figure S6), and the same results were also observed in the hydroponics experiments conducted by Kusano et al (2020) and Zhai et al (2013). Generally, plants mainly rely on chloroplasts in leaves for photosynthesis rather than roots (Hassan et al, 2022). However, when roots are exposed to continuous light, their potential photosynthetic system will be stimulated (Kusano et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

CsBPC2 is a key regulator of root growth and development

Meng

et al. 2023

Physiologia Plantarum

View full text Add to dashboard Cite

BASIC PENTACYSTEINE (BPCs) transcription factors are important regulators of plant growth and development. However, the regulatory mechanism of BPC2 in roots remains unclear. In our previous study, we created Csbpc2 cucumber mutants by the CRISPR/Cas9 system, and our studies on the phenotype of Csbpc2 mutants showed that the root growth was inhibited compared with wide‐type (WT). Moreover, the surface area, volume and number of roots decreased significantly, with root system architecture changing from dichotomous branching to herringbone branching. Compared with WT, the leaf growth of the Csbpc2 mutants was not affected. However, the palisade and spongy tissue were significantly thinner, which was not beneficial for photosynthesis. The metabolome of root exudates showed that compared with WT, amino acids and their derivatives were significantly decreased, and the enriched pathways were mainly regulated by amino acids and their derivatives, indicating that knockout of CsBPC2 mainly affected the amino acid content in root exudates. Importantly, transcriptome analysis showed that knockout of CsBPC2 mainly affected root gene expression. Knockout of CsBPC2 significantly reduced the gene expression of gibberellins synthesis. However, the expression of genes related to amino acid synthesis, nitrogen fixation and PSII‐related photosynthesis increased significantly, which may be due to the effect of knocking out CsBPC2 on gibberellins synthesis, resulting in the inhibition of seedling growth, thus forming negative feedback regulation. Generally, we showed for the first time that BPC2 is a key regulator gene of root growth and development, laying the foundation for future mechanisms of BPC2 regulation in roots.

show abstract

Section: Discussionmentioning

confidence: 99%

CsBPC2 is a key regulator of root growth and development

Meng

et al. 2023

Physiologia Plantarum

View full text Add to dashboard Cite

show abstract

“…The modules from A. thaliana were considered together with the 14 modules of coexpressed genes identified by Hassan et al [12] from RNA-seq of A. halleri roots grown under Cd stress and in control conditions. All module eigengenes, considered representative of the expression pattern of the genes within each module, were used to identify the modules showing the most statistically significant difference of expression between the Cd-treatment versus the control.…”

Section: Discussionmentioning

confidence: 99%

“…Module eigengenes (MEs), representative of the expression pattern of each group o co-expressed genes (module), were used to identify modules with the most significan variation of the expression pattern between treatment (Cd stress) and the control. This approach was applied both to A. thaliana root modules and also to the A. halleri root mod ules identified by Hassan and colleagues [12]. The results of this analysis allowed the se lection of the lightblue4 module (corr = 0.87; p-value = 0.023) and the antiquewhite1 mod ule (corr = −0.88; p-value = 0.01789) for A. thaliana root and of the brown module (corr = 0.938; p-value = 1.3 × 10 −11 ) and the plum1 module (corr = −0.924; p-value = 1.33 × 10 −10 ) for A. halleri (Figure 4).…”

Section: Identification Of Modules Associated With Cadmium In a Thali...mentioning

confidence: 99%

“…However, the relationship between all these factors remains Plants 2023, 12, 1793 2 of 19 unclear, differing with species, plant organs, heavy metal concentrations, and treatment durations (reviewed in [8]). Recently, Arabidopsis halleri gained attention for its constitutivee tolerance to zinc (Zn) and Cd and for its close phylogenetic relationship to the model plant A. thaliana; thus, it is now emerging as a promising model to study heavy metal hyperaccumulation traits [10][11][12]. Despite this evolutionary closeness between A. halleri and A. thaliana, the main mechanisms for tolerating metal stress are specific to one or the other species and therefore may be based on some different and particular biological processes, or the activation of them according to species-specific patterns.…”

Section: Introductionmentioning

confidence: 99%

“…These holistic approaches resolve some problems associated with the traditional methods based on the comparison of group pairs, such as differentially expressed gene (DEG) analysis, and thus have more advantages than traditional methods, being able to comprehensively explore the associations between genes and target traits [29]. Among a variety of methods applied to infer networks, weighted gene co-expression network analysis (WGCNA) has shown its potential in developing an understanding of the relationships among genes and in focusing on specific modules of co-expressed genes and key genes correlated with specific phenotypes and, thus, have been used to select targets or to characterize traits [12,30,31]. Additionally, expression data can be analyzed by traditional methods based on pairwise comparisons to identify the statistically significant variations of the expression patterns to profile traits, uncover targets, or focus on specific biomarkers in plants [32,33].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

Sferra

Fantozzi

Scippa

et al. 2023

Plants

Self Cite

View full text Add to dashboard Cite

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.

show abstract