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<p><i>Toona fargesii</i> A. Chev., a tree species endemic to China and of high economic value, is classified as endangered. This species regenerates mainly via root sprouting, an asexual strategy potentially reducing forest genetic diversity. Yet, the genetic regulation of root sprouting has been still poorly characterized. To elucidate the underlying mechanisms, root sprouting (RS) and non-root sprouting (NRS) samples were distinguished based on morphological observations and subjected to transcriptome sequencing covering mRNA, lncRNA, and miRNA. Comparative analysis identified 2,603 differentially expressed genes (DEGs), 135 differentially expressed long non-coding RNAs (DELs), and 893 differentially expressed miRNAs (DEMs). DEGs were significantly enriched in pathways such as ABC transporters and photosynthesis, implying that root sprouting may involve hormone‑mediated regulation and light-responsive intermediates. Notably, <i>SQUAMOSA-PROMOTER BINDING PROTEIN-like</i> (<i>SPL10</i>) and <i>BRANCHED1</i> (<i>BRC1</i>) which reportedly orchestrated hormones were significantly identified among DEGs. These two genes, together with their upstream regulatory <i>miR156</i> and <i>miR319</i>, were integrated as hub nodes to construct a miRNA-mRNA-lncRNA network. Within this network, the <i>miR319</i>-<i>BRC1</i>-<i>miR156</i>-<i>SPL10</i>-<i>lncRNA</i>s module was identified as a potential genetic regulatory network governing root sprouting development. Collectively, our transcriptomic analysis elucidates potential regulatory mechanisms underlying root sprouting and provides insights into the reproductive strategy of the endangered <i>T. fargesii</i>.</p>

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Integrative miRNA-mRNA-lncRNA Analysis Unveils Regulatory Networks Involved Clonal Reproduction of Root Sprouting in Toona fargesii

  • 期刊论文

  • 发表日期：

    2026年2月17日

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  • Jiaming Tie,
  • Qiangqiang Li,
  • Qiangqiang Cheng,
  • Qiuwei Zhong,
  • Zhonghua Tu,
  • Rongxi Sun,
  • Yao Xiao,
  • Chunce Guo,
  • Lu Zhang,
  • Jikai Ma

摘要

Toona fargesii A. Chev., a tree species endemic to China and of high economic value, is classified as endangered. This species regenerates mainly via root sprouting, an asexual strategy potentially reducing forest genetic diversity. Yet, the genetic regulation of root sprouting has been still poorly characterized. To elucidate the underlying mechanisms, root sprouting (RS) and non-root sprouting (NRS) samples were distinguished based on morphological observations and subjected to transcriptome sequencing covering mRNA, lncRNA, and miRNA. Comparative analysis identified 2,603 differentially expressed genes (DEGs), 135 differentially expressed long non-coding RNAs (DELs), and 893 differentially expressed miRNAs (DEMs). DEGs were significantly enriched in pathways such as ABC transporters and photosynthesis, implying that root sprouting may involve hormone‑mediated regulation and light-responsive intermediates. Notably, SQUAMOSA-PROMOTER BINDING PROTEIN-like (SPL10) and BRANCHED1 (BRC1) which reportedly orchestrated hormones were significantly identified among DEGs. These two genes, together with their upstream regulatory miR156 and miR319, were integrated as hub nodes to construct a miRNA-mRNA-lncRNA network. Within this network, the miR319-BRC1-miR156-SPL10-lncRNAs module was identified as a potential genetic regulatory network governing root sprouting development. Collectively, our transcriptomic analysis elucidates potential regulatory mechanisms underlying root sprouting and provides insights into the reproductive strategy of the endangered T. fargesii.