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<p>Proline-rich receptor kinases perform an important part in regulating several plant metabolic processes and signaling pathways, particularly under biotic and abiotic stress. Although the <i>PERK</i> genes have been found in several agriculturally important species, their characterization in cereal crops remains limited. In this study, we performed a comprehensive genome-wide search to identify unique <i>PERK</i> genes in the rice genome. The computational analysis revealed eight <i>PERK</i>-encoding non-redundant genes distributed across all rice chromosomes. Phylogenetic analysis classified the <i>PERK</i> proteins into five distinct clades suggesting that the <i>PERK</i> gene family has undergone extensive evolutionary diversification and introns loss. In addition to a universally conserved signature <i>PERK</i> domain four group-specific conserved domains and 10 distinct motifs were identified. Gene Duplication study revealed that both segmental and tandem duplication events have helped bring about the expansion of this gene family with purifying selection acting on paralogous genes. A total of 12 types of RNA editing events were identified, encompassing all possible intra-base conversions. The allocation of RNA editing sites (RES) and the resulting amino acid substitutions was determined in chloroplast and mitochondrial genes. <i>Insilco</i> expression profiling using transcriptome data demonstrated tissue-specific expression patterns of <i>OsPERK</i> genes across seed, young and mature leaf, seedling root, and inflorescence. Transcriptomic analysis under salt revealed a significant upregulation of <i>OsPERK</i>1, 2, 5, and 8 indicating that they participate in stress response pathways that are preserved. These findings establish a strong basis for the upcoming functional characterization of <i>PERK</i> genes, particularly within the context of plant response to environmental stresses.</p>

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Prediction of RNA editing sites and genome-wide characterization and identification of PERK gene family in Oryza sativa in response to salinity stress

  • 期刊论文

  • 发表日期：

    2025年7月28日

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  • Hafiz Muhammad Waqas,
  • Muhammad Abu Bakar Saddique,
  • Sajid Fiaz,
  • Afnan A. Alnufaei,
  • Muhammad Ali Sher,
  • Badr Alharthi,
  • Muhammad Hammad Nadeem Tahir,
  • Mahmood Alam Khan,
  • Shahmeer Shahid,
  • Seung Hwan Yang

摘要

Proline-rich receptor kinases perform an important part in regulating several plant metabolic processes and signaling pathways, particularly under biotic and abiotic stress. Although the PERK genes have been found in several agriculturally important species, their characterization in cereal crops remains limited. In this study, we performed a comprehensive genome-wide search to identify unique PERK genes in the rice genome. The computational analysis revealed eight PERK-encoding non-redundant genes distributed across all rice chromosomes. Phylogenetic analysis classified the PERK proteins into five distinct clades suggesting that the PERK gene family has undergone extensive evolutionary diversification and introns loss. In addition to a universally conserved signature PERK domain four group-specific conserved domains and 10 distinct motifs were identified. Gene Duplication study revealed that both segmental and tandem duplication events have helped bring about the expansion of this gene family with purifying selection acting on paralogous genes. A total of 12 types of RNA editing events were identified, encompassing all possible intra-base conversions. The allocation of RNA editing sites (RES) and the resulting amino acid substitutions was determined in chloroplast and mitochondrial genes. Insilco expression profiling using transcriptome data demonstrated tissue-specific expression patterns of OsPERK genes across seed, young and mature leaf, seedling root, and inflorescence. Transcriptomic analysis under salt revealed a significant upregulation of OsPERK1, 2, 5, and 8 indicating that they participate in stress response pathways that are preserved. These findings establish a strong basis for the upcoming functional characterization of PERK genes, particularly within the context of plant response to environmental stresses.