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<p>The serine carboxypeptidase-like protein <i>(SCPL)</i> family is thought to play roles in pathogen defense, stress response, hormonal signaling, and plant development, as suggested by research in other species. However, in case of tomato (<i>Solanum lycopersicum</i>) the identification of genes of <i>SCPL</i> family and the analysis of their functions has not been performed. This comprehensive analysis of <i>SCPL</i> gene family in tomato was performed via various bioinformatics tools and methods including phylogenetic, gene structure, exon intron, conserved motif, evolutionary, expression, gene ontology &amp; protein–protein interaction analysis. In the current study, 53 members of the <i>SCPL</i> gene family have been identified in tomato. The members of <i>SCPL</i> gene family were further divided into three subgroups; i.e., CPI, CPII and CPIII on the basis of structural features. In tomato the 53 <i>SlSCPL</i> genes were located on 11 chromosomes and were widely distributed in the cells. Duplication analysis of the genes revealed that ~ 64.7% were formed by tandem duplication and ~ 35.3% of the members of <i>SCPL</i> were the result of segmental duplication. The duplicated gene pairs of <i>SlSCPL</i> depicted a range of Ka/Ks ratios between 0.61 and 1.86 suggesting the action of both positive and purifying selection. Synteny analysis showed that the <i>SCPL</i> gene expression is significantly influenced by tendom and segmental duplication. The structural analysis of genes showed the existence of multiple introns on most of the <i>SlSCPL</i> genes and relatively conserved motifs in each subfamily. Expression profiling revealed that several <i>SlSCPL</i> genes are differentially regulated under drought and heat stress, suggesting potential roles in abiotic stress responses. In this study the cis-acting elements analysis revealed that the <i>SCPL</i> genes’ promoter sequence are useful in response to light, MeJA, ABA responsive elements and plant growth responsiveness. Obtained results from this study provide comprehensive investigation of tomato <i>SCPL</i> genes potentially beneficial for future research regarding improvement of heat and drought tolerance.</p>

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A genome-wide approach to the comprehensive analysis of the serine carboxypeptidase-like protein family in Solanum lysopersicum L.

  • 期刊论文

  • 发表日期：

    2025年7月23日

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  • Arshad Jamil,
  • M. A. Habib,
  • Ahmed B. M. Ibrahim,
  • Bushra Ahmad,
  • Muhammad Zulfiqar Ahmad,
  • Jamal Abdul Nasir

摘要

The serine carboxypeptidase-like protein (SCPL) family is thought to play roles in pathogen defense, stress response, hormonal signaling, and plant development, as suggested by research in other species. However, in case of tomato (Solanum lycopersicum) the identification of genes of SCPL family and the analysis of their functions has not been performed. This comprehensive analysis of SCPL gene family in tomato was performed via various bioinformatics tools and methods including phylogenetic, gene structure, exon intron, conserved motif, evolutionary, expression, gene ontology & protein–protein interaction analysis. In the current study, 53 members of the SCPL gene family have been identified in tomato. The members of SCPL gene family were further divided into three subgroups; i.e., CPI, CPII and CPIII on the basis of structural features. In tomato the 53 SlSCPL genes were located on 11 chromosomes and were widely distributed in the cells. Duplication analysis of the genes revealed that ~ 64.7% were formed by tandem duplication and ~ 35.3% of the members of SCPL were the result of segmental duplication. The duplicated gene pairs of SlSCPL depicted a range of Ka/Ks ratios between 0.61 and 1.86 suggesting the action of both positive and purifying selection. Synteny analysis showed that the SCPL gene expression is significantly influenced by tendom and segmental duplication. The structural analysis of genes showed the existence of multiple introns on most of the SlSCPL genes and relatively conserved motifs in each subfamily. Expression profiling revealed that several SlSCPL genes are differentially regulated under drought and heat stress, suggesting potential roles in abiotic stress responses. In this study the cis-acting elements analysis revealed that the SCPL genes’ promoter sequence are useful in response to light, MeJA, ABA responsive elements and plant growth responsiveness. Obtained results from this study provide comprehensive investigation of tomato SCPL genes potentially beneficial for future research regarding improvement of heat and drought tolerance.