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

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dc.authoridAhmad, Furqan/0000-0002-5328-2174
dc.authoridAli, Zulfiqar/0000-0003-1228-3338
dc.authoridUr Rehman, Shoaib/0000-0002-9462-699X
dc.contributor.authorShahid, Shahmeer
dc.contributor.authorSher, Muhammad Ali
dc.contributor.authorAhmad, Furqan
dc.contributor.authorRehman, Shoaib Ur
dc.contributor.authorFarid, Babar
dc.contributor.authorRaza, Humayun
dc.contributor.authorAli, Zulfiqar
dc.date.accessioned2024-11-07T13:35:24Z
dc.date.available2024-11-07T13:35:24Z
dc.date.issued2022
dc.departmentNiğde Ömer Halisdemir Üniversitesi
dc.description.abstractObjectives: Inadvertent climate changes continuously threating the crops production and thus affecting the livelihood of peoples across the world. The maize production at world level has severely been hampered by the drought stress. Proline-rich extensin-like receptor kinases (PERKs) are considered among the sub-class of plants larger protein family, receptor kinases. Member of PERK gene family play significant role in both abiotic and biotic stress and in various plant metabolic activities and pathways.Methods: As of now, no comprehensive research is reported for PERK genes in maize. We have performed a genome wide in-silico analysis and identify twenty-three PERK genes in maize. We performed phylogenetic analysis, sequence logos, motif analysis, promoter analysis, chromosomal and subcellular localization, synteny and expression analysis using RNA seq data under drought stress. We also predict RNA editing sites in mitochondrial and chloroplast genome.Results: Phylogenetic study of PERK genes from eight different plant species divided into four distinct clades. Four subclasses group of ZmPERKs were observed based on domain organization, motif pattern, and phylogenetic analysis. The exon-intron arrangement of the ZmPERK were conserved among members of the same subclasses. In the promoter region different cis-elements were found those were involved in the growth and development, as well as light and stress response. Through gene duplication analysis it was observed that segmental duplications in ZmPERKs played major role in maize evolution. The Ka/Ks ratios indicated that most ZmPERK genes during the evolution have experienced strong purifying selection. The conversion of cytosine (C) to uracil (U) was observed in all predicted editing sites (U). These transitions were mostly based on changes in the first and second codon bases. The in-silico expression analysis of transcriptome data revealed the differential expression of ZmPERK genes in response to drought stress and oil content accumulation.Conclusion: The current study provides base information on the PERK gene family in maize. Our findings can serve as a reference for further functional analysis of ZmPERKs. These genes can be further explored and used in breeding program to develop cultivars resilient to drought stress. (c) 2022 The Authors. Published by Elsevier B.V. on behalf of King Saud University. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
dc.description.sponsorshipKing Saud University, Riyadh, Saudi Arabia [RSP-2023R7]
dc.description.sponsorshipThis project was supported by Researchers Supporting Project Number (RSP-2023R7) King Saud University, Riyadh, Saudi Arabia.
dc.identifier.doi10.1016/j.jksus.2022.102293
dc.identifier.issn1018-3647
dc.identifier.issn2213-686X
dc.identifier.issue8
dc.identifier.scopus2-s2.0-85137697432
dc.identifier.scopusqualityQ1
dc.identifier.urihttps://doi.org/10.1016/j.jksus.2022.102293
dc.identifier.urihttps://hdl.handle.net/11480/16474
dc.identifier.volume34
dc.identifier.wosWOS:000883723600001
dc.identifier.wosqualityQ2
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.language.isoen
dc.publisherElsevier
dc.relation.ispartofJournal of King Saud University Science
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.snmzKA_20241106
dc.subjectPERK
dc.subjectGenome wide analysis
dc.subjectRNA editing sites drought
dc.subjectOil content
dc.titlePrediction of RNA editing sites and genome-wide characterization of PERK gene family in maize (Zea mays L.) in response to drought stress
dc.typeArticle

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