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

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.