Prediction of RNA editing sites and genome-wide characterization of PERK gene family in maize (Zea mays L.) in response to drought stress

Shahid, Shahmeer; Sher, Muhammad; Ahmad, Furqan; Rehman, Shoaib Ur; Farid, Babar; Raza, Humayun; Ali, Zulfiqar; Maqbool, Amir; Al‐Farraj, Saleh A.; Ansari, Mohammad Javed

doi:10.1016/j.jksus.2022.102293

Journal of King Saud University - Science

2022

DOI: 10.1016/j.jksus.2022.102293

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Prediction of RNA editing sites and genome-wide characterization of PERK gene family in maize (Zea mays L.) in response to drought stress

Shahmeer Shahid

Muhammad Sher²,

Furqan Ahmad³

et al.

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2024

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Cited by 2 publications

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Genome-wide analysis and prediction of chloroplast and mitochondrial RNA editing sites of AGC gene family in cotton (Gossypium hirsutum L.) for abiotic stress tolerance

Ahmad,

Abdullah,

Khan

et al. 2024

BMC Plant Biol

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Background Cotton is one of the topmost fiber crops throughout the globe. During the last decade, abrupt changes in the climate resulted in drought, heat, and salinity. These stresses have seriously affected cotton production and significant losses all over the textile industry. The GhAGC kinase, a subfamily of AGC group and member of serine/threonine (Ser/Thr) protein kinases group and is highly conserved among eukaryotic organisms. The AGC kinases are compulsory elements of cell development, metabolic processes, and cell death in mammalian systems. The investigation of RNA editing sites within the organelle genomes of multicellular vascular plants, such as Gossypium hirsutum holds significant importance in understanding the regulation of gene expression at the post-transcriptional level. Methods In present work, we characterized twenty-eight GhAGC genes in cotton and constructed phylogenetic tree using nine different species from the most primitive to the most recent. Results In sequence logos analyses, highly conserved amino acid residues were found in G. hirsutum , G. arboretum , G. raimondii and A. thaliana . The occurrence of cis-acting growth and stress-related elements in the promoter regions of GhAGCs highlight the significance of these factors in plant development and abiotic stress tolerance. Ka/Ks levels demonstrated that purifying selection pressure resulting from segmental events was applied to GhAGC with little functional divergence. We focused on identifying RNA editing sites in G. hirsutum organelles, specifically in the chloroplast and mitochondria, across all 28 AGC genes. Conclusion The positive role of GhAGCs was explored by quantifying the expression in the plant tissues under abiotic stress. These findings help in understanding the role of GhAGC genes under abiotic stresses which may further be used in cotton breeding for the development of climate smart varieties in abruptly changing climate. Supplementary Information The online version contains supplementary material available at 10.1186/s12870-024-05598-0.

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Genome-wide analysis and prediction of chloroplast and mitochondrial RNA editing sites of AGC gene family in cotton (Gossypium hirsutum L.) for abiotic stress tolerance

Ahmad,

Abdullah,

Khan

et al. 2024

BMC Plant Biol

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Characterization of Strubbelig-Receptor Family (SRF) Related to Drought and Heat Stress Tolerance in Upland Cotton (Gossypium hirsutum L.)

Ahmad,

Rehman,

Rahman

et al. 2024

Agronomy

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Cotton is one of the world’s leading fiber crops, but climate change, drought, heat, and salinity have significantly decreased its production, consequently affecting the textile industries globally. To acclimate to these environmental challenges, a number of gene families involved in various molecular, physiological, and hormonal mechanisms play crucial roles in improving plants response to various abiotic stresses. One such gene family is the GhSRF, a Strubbelig-Receptor family (SRF), and member of the leucine-rich repeat (LRR-V) group. This family encodes leucine-rich repeat transmembrane receptor-like kinases (LRR-RLKs) and have not yet been explored in cotton. Arabidopsis thaliana Strubbelig-Receptor gene sequences were used as queries to identify the homologs in cotton, with subsequent support from the literature and functional prediction through online data. In the current study, a comprehensive genome-wide analysis of cotton was conducted, identifying 22 SRF putative proteins encoded by 22 genes. We performed the detailed analysis of these proteins, including phylogeny, motif and gene structure characterization, promoter analysis, gene mapping on chromosomes, gene duplication events, and chromosomal sub-cellular localization. Expression analysis of putative genes was performed under drought and heat stress conditions using publicly available RNAseq data. The qRT-PCR results showed elevated expression of GhSRF2, GhSRF3, GhSRF4, GhSRF10, and GhSRF22 under drought and heat stress. So, it could be speculated that these genes may play a role in drought and heat tolerance in cotton. These findings could be helpful in cotton breeding programs for the development of climate-resilient cultivars.

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Prediction of RNA editing sites and genome-wide characterization of PERK gene family in maize (Zea mays L.) in response to drought stress

Cited by 2 publications

References 36 publications

Genome-wide analysis and prediction of chloroplast and mitochondrial RNA editing sites of AGC gene family in cotton (Gossypium hirsutum L.) for abiotic stress tolerance

Genome-wide analysis and prediction of chloroplast and mitochondrial RNA editing sites of AGC gene family in cotton (Gossypium hirsutum L.) for abiotic stress tolerance

Characterization of Strubbelig-Receptor Family (SRF) Related to Drought and Heat Stress Tolerance in Upland Cotton (Gossypium hirsutum L.)

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