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<p>Dirigent (DIR) proteins play a crucial role in regulating plant growth, development, and stress responses. In this&#xa0;study, we conducted a comprehensive genome-wide analysis of the <i>DIR</i> gene family in <i>Arabidopsis thaliana</i>, <i>Brassica rapa</i>, <i>B. oleracea</i>, and <i>B. napus</i>. We identified 26 <i>DIR</i> genes in <i>A. thaliana</i>, 36 in <i>B. rapa</i>, 70 in <i>B. napus</i>, and 34 in <i>B. oleracea</i>, which were classified into three phylogenetic clades: a, b/d, and e. Segmental and whole-genome duplication events significantly contributed to the expansion of <i>DIR</i> genes in the <i>Brassicaceae</i> family, although more than half of the <i>DIR</i> genes were lost in <i>B. napus</i>, <i>B. oleracea</i>, and <i>B. rapa</i> during evolution. Most of the Duplicated genes experienced purifying (negative) selection, indicating functional conservation. <i>DIR</i> gene evolution was also influenced by Weak codon usage bias and strong mutational pressure. Analysis of promoter regions revealed diverse <i>cis</i>-regulatory elements and miRNA-mediated regulation, suggesting a complex regulatory network. RNA-seq data demonstrated tissue-specific expression patterns of <i>BnDIR</i> genes, particularly in roots and seeds. Furthermore, qRT-PCR analysis showed that <i>BnDIR12</i>, <i>BnDIR19</i>, and <i>BnDIR39</i> were significantly up-regulated under salt and drought stress, indicating their potential role in enhancing stress tolerance. Overall, this study provides valuable insights into the evolution, regulation, and functional roles of <i>DIR</i> genes in improving the resilience of <i>Brassica</i> crops.</p>

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Comprehensive genome wide analysis of the dirigent (DIR) gene family in Arabidopsis thaliana and Brassica species: evolutionary dynamics and abiotic stress response mechanisms

  • 期刊论文

  • 发表日期：

    2025年6月14日

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  • Lei Zhang,
  • Min Sun,
  • Hai Zhang

摘要

Dirigent (DIR) proteins play a crucial role in regulating plant growth, development, and stress responses. In this study, we conducted a comprehensive genome-wide analysis of the DIR gene family in Arabidopsis thaliana, Brassica rapa, B. oleracea, and B. napus. We identified 26 DIR genes in A. thaliana, 36 in B. rapa, 70 in B. napus, and 34 in B. oleracea, which were classified into three phylogenetic clades: a, b/d, and e. Segmental and whole-genome duplication events significantly contributed to the expansion of DIR genes in the Brassicaceae family, although more than half of the DIR genes were lost in B. napus, B. oleracea, and B. rapa during evolution. Most of the Duplicated genes experienced purifying (negative) selection, indicating functional conservation. DIR gene evolution was also influenced by Weak codon usage bias and strong mutational pressure. Analysis of promoter regions revealed diverse cis-regulatory elements and miRNA-mediated regulation, suggesting a complex regulatory network. RNA-seq data demonstrated tissue-specific expression patterns of BnDIR genes, particularly in roots and seeds. Furthermore, qRT-PCR analysis showed that BnDIR12, BnDIR19, and BnDIR39 were significantly up-regulated under salt and drought stress, indicating their potential role in enhancing stress tolerance. Overall, this study provides valuable insights into the evolution, regulation, and functional roles of DIR genes in improving the resilience of Brassica crops.