Stress-responsive transcription factor families are key components of the core abiotic stress response in maize

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 20, 2025

ABSTRACT Abiotic stresses, including drought, salt, heat, cold, flooding, and low nitrogen, have devastating impacts on agriculture are increasing in frequency globally due to climate change. Plants can experience multiple abiotic stresses simultaneously or sequentially within a single growing season, combinatorial elicit shared overlapping molecular physiological responses. Here, we searched for core stress responsive genes maize across diverse stressors through meta-analysis of public RNAseq data. Our analysis revealed significant heterogeneity gene expression datasets factors such as tissue type, genotype, experimental conditions, which mitigated batch correction. Using nearly 1,900 samples with both traditional set operations novel random forest machine learning approach, identified 744 stress-responsive the six stresses. These enriched transcription factors, families AP2/ERF-ERF, NAC, bZIP, HSF, C2C2-CO-like. Co-expression network demonstrated that these TFs co-expressed stress-specific peripheral genes, supporting their role regulating generalized results suggest employs conserved yet flexible transcriptional strategy respond acting potential regulators universal pathways. findings provide valuable resource understanding tolerance mechanisms guiding future breeding engineering efforts enhance resilience under

Language: Английский

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Meta-analysis of RNA-seq data of soybean under heat, water, and drought stresses

Plant Biotechnology Reports, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 22, 2025

Language: Английский

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Recent Advances in Genome Editing and Bioinformatics: Addressing Challenges in Genome Editing Implementation and Genome Sequencing

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(7), P. 3442 - 3442

Published: April 7, 2025

Genome-editing technology has advanced significantly since the 2020 Nobel Prize in Chemistry was awarded for development of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9). While CRISPR-Cas9 become widely used academic research, its social implementation lagged due to unresolved patent disputes slower progress gene function analysis. To address this, new approaches bypassing direct analysis are needed, with bioinformatics next-generation sequencing (NGS) playing crucial roles. NGS is essential genome target species, but challenges such as data quality, heterogeneity, ploidy, small individual sizes persist. Despite these issues, advancements technologies, like PacBio high-fidelity (HiFi) long reads high-throughput chromosome conformation capture (Hi-C), have improved sequencing. Bioinformatics contributes editing through off-target prediction selection, both which require accurate sequence information. In this review, I will give updates on technologies a focus rapid

Language: Английский

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Genome‐wide characterization and expression analysis of GATA transcription factors under combination of light wavelengths and drought stress in potato

Plant Direct, Journal Year: 2024, Volume and Issue: 8(4)

Published: April 1, 2024

Abstract GATA is one of the prominent transcription factor families conserved among many organisms in eukaryotes and has different biological roles pathways, particularly light regulation plants. Although factors (TFs) have been identified crop species, their abiotic stress tolerance not studied potato. In this study, we 32 TFs potato ( Solanum tuberosum ) by silico analyses, expression levels selected six genes were investigated drought‐tolerant (Sante) sensitive (Agria) cultivars under light, drought, combined (light + drought) conditions. According to phylogenetic results, StGATA divided into four main groups (I, II, III, IV) sub‐groups I II (eight five, respectively). uniformly localized each chromosome with a exon/intron structure. The presence cis‐ elements within family further supported possible involvement response, tissue‐specific expression, hormonal regulation. Additional PPI investigations showed that these networks, especially for Groups I, IV, play significant role response drought stress. Six s chosen from expressional profiling, both Sante Agria was mainly downregulated purple red lights, (blue drought). interactomes StGATAs, StGATA3 , StGATA24 StGATA29 analyzed, accessions motifs checked expression. results target proteins, cyclin‐P3‐1, SPX domain‐containing protein 1, mitochondrial calcium uniporter 2, mitogen‐activated kinase YODA, splicing 3 B subunit 4‐like, phytochrome‐mediated stomatal patterning, development, activity. Understanding interactions between mechanisms plants essential. It will eventually be enhance resilience climate change manipulating pathways.

Language: Английский

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Meta-analysis of public RNA-sequencing data of drought and salt stresses in different phenotypes ofOryza sativa

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 8, 2024

Abstract Environmental stresses, such as drought and salt, adversely affect plant growth crop productivity. While many studies have focused on established components of stress signaling pathways, research unknown elements remains limited. In this study, we collected RNA sequencing (RNA-Seq) data from Oryza sativa registered in public databases conducted a meta-analysis integrating multiple studies. We analyzed 105 paired RNA-Seq datasets resistant or susceptible cultivars under salt conditions to identify novel stress-responsive genes with common expression changes across these datasets. A identified 10 specifically upregulated 12 both conditions. Furthermore, by comparing previously Arabidopsis thaliana , explored potentially involved response mechanisms that are conserved species. The data-driven study may serve targets for future genome editing.

Language: Английский

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Identification and functional categorization of the most stably and most variably expressed genes and retained introns in Arabidopsis thaliana seedlings

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 27, 2024

Abstract We used a large, uniform, RNA-seq dataset to investigate the stability of gene expression and intron retention in Arabidopsis thaliana seedlings. Functional classification most stably variably expressed genes was determined by GO enrichment analyses. Many encoded proteins involved photosynthesis chloroplast structure, likely reflecting their sensitivity changeable light intensities, stress responses, which allow plants cope with environmental challenges. As revealed analysis, were protein, lipid vesicle trafficking, suggesting that fluctuations these are suboptimal for normal seedling development. analyses containing either usually retained or spliced introns no consistent enrichments any specific functional categories. However, highly often located first last position, may contain 5’ 3’ UTRs necessary transcriptional regulation mRNA transport stability. Conversely, more frequently internal portions pre-mRNAs, indicating reliable splicing coding regions is needed prevent formation premature stop codons. The large we generated can be useful investigating additional aspects pre-mRNA seedlings sets precedent future scale transcriptome

Language: Английский

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