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<p><i>Astragalus sinicus</i> (Chinese milkvetch) is a legume crop of major economic and ecological importance, regularly employed in sustainable farming to enhance soil nitrogen. Despite its significance, plastome structural dynamics within the Inverted Repeat-Lacking Clade (IRLC) of Fabaceae remain poorly understood, and pan-plastome resources for this species are lacking. Here, we present a pan-plastome for <i>A. sinicus</i> using 140 resequenced individuals. Our analysis reveals a unique evolutionary trajectory characterized by repeat-mediated recombination rather than the retention of a traditional quadripartite structure or simple IR loss. We identify a specific ~1.2 kb repeat unit that facilitates a localized recombination event, leading to the duplication of the tRNA gene <i>trnQ-UUG</i>. While typically a single-copy gene in other Fabaceae, <i>trnQ-UUG</i> exists in two copies within the recombined regions of <i>A. sinicus</i>. Furthermore, population genomic analyses resolve the 140 individuals into five differentiated maternal genetic lineages (G1–G5). Fixed non-synonymous substitutions in key photosynthetic genes (<i>psbM</i>, <i>psaI</i>) serve as molecular signatures differentiating the ancestral lineage from derived groups. These findings offer a refined model for plastome structural evolution via localized recombination and provide essential genomic resources for the germplasm evaluation and genetic improvement of this industrial crop.</p>

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Contraction, recombination and innovation shape the dynamic pan-plastome of Astragalus sinicus

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月2日

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  • Wen Ge,
  • Zhibing Li,
  • Luyao Wang,
  • Luke R. Tembrock,
  • Yingying Xiao,
  • Shiyun Han,
  • Jianke Yang,
  • Penghao Wang,
  • Shoubiao Zhou,
  • Zhiqiang Wu,
  • Junhu Kan

摘要

Astragalus sinicus (Chinese milkvetch) is a legume crop of major economic and ecological importance, regularly employed in sustainable farming to enhance soil nitrogen. Despite its significance, plastome structural dynamics within the Inverted Repeat-Lacking Clade (IRLC) of Fabaceae remain poorly understood, and pan-plastome resources for this species are lacking. Here, we present a pan-plastome for A. sinicus using 140 resequenced individuals. Our analysis reveals a unique evolutionary trajectory characterized by repeat-mediated recombination rather than the retention of a traditional quadripartite structure or simple IR loss. We identify a specific ~1.2 kb repeat unit that facilitates a localized recombination event, leading to the duplication of the tRNA gene trnQ-UUG. While typically a single-copy gene in other Fabaceae, trnQ-UUG exists in two copies within the recombined regions of A. sinicus. Furthermore, population genomic analyses resolve the 140 individuals into five differentiated maternal genetic lineages (G1–G5). Fixed non-synonymous substitutions in key photosynthetic genes (psbM, psaI) serve as molecular signatures differentiating the ancestral lineage from derived groups. These findings offer a refined model for plastome structural evolution via localized recombination and provide essential genomic resources for the germplasm evaluation and genetic improvement of this industrial crop.