Scholarlink

<p>Allopolyploidization is a major driver of plant evolution and crop improvement, influencing both adaptation and diversification. MicroRNAs (miRNAs), 20–24&#xa0;nt endogenous noncoding RNAs, regulate post-transcriptional gene expression and influence diverse biological processes. MiRNAs regulate a variety of agronomic traits and represent an important genetic resource for crop genetic improvement. While prevalent in plant evolution, the short-term (&lt; 10,000&#xa0;years) impact of allopolyploidization on miRNA evolution remains unclear. This study systematically compared miRNAs in the A genomes of <i>Brassica rapa</i>, <i>Brassica juncea</i>, and <i>Brassica napus</i> to reveal the short-term effects of allopolyploidization on miRNAs. The results showed that allopolyploidization caused loss of over half of the miRNAs in the A genomes of <i>B. juncea</i> and <i>B. napus</i> and accelerated miRNA cluster loss. The subgenome dominance (LF &gt; MF1/MF2) resulting from ancient whole-genome triplication persisted post-allopolyploidization. Following allopolyploidization, the nucleotide divergence of miRNAs did not change significantly, and the maximum nucleotide divergence was only 0.11. Multi-copy miRNA retention rates differ between <i>B. juncea</i> and <i>B. napus</i>, potentially due to the influence of B and C genomes. MiRNA retention was affected by flanking protein-coding genes, with those adjacent to multi-copy protein-coding genes more likely retained as multiple copies post-allopolyploidization. Retained single miRNAs may form miRNA clusters via tandem duplication events. Additionally, homoeologous exchanges may affect the protein-coding genes flanking miRNAs. These findings indicated that short-term allopolyploidization significantly affected miRNA retention in <i>Brassica</i> A genome, providing new insights into allopolyploidization impacts on miRNA evolution.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

Allopolyploidization-driven short-term evolution of miRNAs in Brassica A genome

  • 期刊论文

  • 发表日期：

    2025年12月26日

查看全文
  • Mengyan Zhang,
  • Guojin Yang,
  • Mingli Yan,
  • Zhixiang Liu,
  • Chaozhen Zeng

摘要

Allopolyploidization is a major driver of plant evolution and crop improvement, influencing both adaptation and diversification. MicroRNAs (miRNAs), 20–24 nt endogenous noncoding RNAs, regulate post-transcriptional gene expression and influence diverse biological processes. MiRNAs regulate a variety of agronomic traits and represent an important genetic resource for crop genetic improvement. While prevalent in plant evolution, the short-term (< 10,000 years) impact of allopolyploidization on miRNA evolution remains unclear. This study systematically compared miRNAs in the A genomes of Brassica rapa, Brassica juncea, and Brassica napus to reveal the short-term effects of allopolyploidization on miRNAs. The results showed that allopolyploidization caused loss of over half of the miRNAs in the A genomes of B. juncea and B. napus and accelerated miRNA cluster loss. The subgenome dominance (LF > MF1/MF2) resulting from ancient whole-genome triplication persisted post-allopolyploidization. Following allopolyploidization, the nucleotide divergence of miRNAs did not change significantly, and the maximum nucleotide divergence was only 0.11. Multi-copy miRNA retention rates differ between B. juncea and B. napus, potentially due to the influence of B and C genomes. MiRNA retention was affected by flanking protein-coding genes, with those adjacent to multi-copy protein-coding genes more likely retained as multiple copies post-allopolyploidization. Retained single miRNAs may form miRNA clusters via tandem duplication events. Additionally, homoeologous exchanges may affect the protein-coding genes flanking miRNAs. These findings indicated that short-term allopolyploidization significantly affected miRNA retention in Brassica A genome, providing new insights into allopolyploidization impacts on miRNA evolution.