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Background <p>The bromodomain (BRD) proteins play a pivotal role in regulating gene expression by recognizing acetylated lysine residues and acting as chromatin-associated post-translational modification-inducing proteins. Although BRD proteins have been extensively studied in mammals, they have also been characterized in plants like <i>Arabidopsis thaliana</i> and <i>Oryza sativa</i>, where they regulate stress-responsive genes related to drought, salinity, and cold. However, their roles in cotton species remain unexplored.</p> Results <p>In this genome-wide comparative analysis, 145 <i>BRD</i> genes were identified in the tetraploid species (<i>Gossypium hirsutum</i> and <i>G. barbadense</i>), compared with 82 <i>BRD</i> genes in their diploid progenitors (<i>G. arboreum</i> and <i>G. raimondii</i>), indicating that polyploidization significantly influenced <i>BRD</i> gene evolution. Gene duplication analysis revealed 78.85% of duplications were segmental and 21.15% were tandem among 104 in-paralogous gene pairs, contributing to <i>BRD</i> gene expansion. Gene structure, motif, and domain analyses demonstrated that most genes were intron-less and conserved throughout evolution. Syntenic analysis revealed a greater number of orthologous gene pairs in the Dt sub-genome than in the At sub-genome. The abundance of regulatory, hormonal, and defense-related <i>cis</i>-regulatory elements in the&#xa0;promoter region suggests that <i>BRD</i> genes play a role in both biotic and abiotic stress responses. Protein-protein interaction analysis indicated that global transcription factor group E&#xa0;(GTE) transcription factors regulate <i>BRD</i> genes. Expression analysis revealed that <i>BRD</i> genes are predominantly involved in ovule development, with some genes displaying specific expression patterns under heat, cold, and salt stress. Furthermore, qRT-PCR analysis demonstrated significant differential expression of <i>BRD</i> genes between the tolerant and sensitive genotype, underscoring their potential role in mediating drought and salinity stress responses.</p> Conclusions <p>This study provides valuable insights into the evolution of <i>BRD</i> genes across species and their roles in abiotic stress tolerance, highlighting their potential in breeding programs to develop drought and salinity tolerant cotton varieties.</p>

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Phylogenomic analysis of bromodomain genes in cotton (Gossypium spp.) and their potential roles in abiotic stress tolerance

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年7月8日

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  • Tayyab Muhammad,
  • Taj Muhammad Hassan,
  • Ahmad Ali Ijaz,
  • Rana Faiza Rehman,
  • Shahzaib Muhammad,
  • Atif Rana Muhammad,
  • Azhar Muhammad Tehseen,
  • Khan Sultan Habibullah,
  • Kakakhel Ishaq Ahmad Mian,
  • He Shoupu,
  • Rana Iqrar Ahmad

摘要

Background

The bromodomain (BRD) proteins play a pivotal role in regulating gene expression by recognizing acetylated lysine residues and acting as chromatin-associated post-translational modification-inducing proteins. Although BRD proteins have been extensively studied in mammals, they have also been characterized in plants like Arabidopsis thaliana and Oryza sativa, where they regulate stress-responsive genes related to drought, salinity, and cold. However, their roles in cotton species remain unexplored.

Results

In this genome-wide comparative analysis, 145 BRD genes were identified in the tetraploid species (Gossypium hirsutum and G. barbadense), compared with 82 BRD genes in their diploid progenitors (G. arboreum and G. raimondii), indicating that polyploidization significantly influenced BRD gene evolution. Gene duplication analysis revealed 78.85% of duplications were segmental and 21.15% were tandem among 104 in-paralogous gene pairs, contributing to BRD gene expansion. Gene structure, motif, and domain analyses demonstrated that most genes were intron-less and conserved throughout evolution. Syntenic analysis revealed a greater number of orthologous gene pairs in the Dt sub-genome than in the At sub-genome. The abundance of regulatory, hormonal, and defense-related cis-regulatory elements in the promoter region suggests that BRD genes play a role in both biotic and abiotic stress responses. Protein-protein interaction analysis indicated that global transcription factor group E (GTE) transcription factors regulate BRD genes. Expression analysis revealed that BRD genes are predominantly involved in ovule development, with some genes displaying specific expression patterns under heat, cold, and salt stress. Furthermore, qRT-PCR analysis demonstrated significant differential expression of BRD genes between the tolerant and sensitive genotype, underscoring their potential role in mediating drought and salinity stress responses.

Conclusions

This study provides valuable insights into the evolution of BRD genes across species and their roles in abiotic stress tolerance, highlighting their potential in breeding programs to develop drought and salinity tolerant cotton varieties.