A Reference Assembly for the Legume Cover Crop Smooth Vetch Vicia villosa Roth var. glabrescens

<i>Vicia villosa</i> Roth var. <i>glabrescens</i> (smooth vetch) is an economically important legume cover crop valued for its nitrogen-fixing capacity, high biomass yield, and adaptability across diverse agroecosystems. Here, we present a chromosome-scale, high-quality genome assembly of <i>V. villosa</i> var. <i>glabrescens</i>, constructed using PacBio HiFi sequencing combined with Hi-C scaffolding. The assembly spans 3.70 Gb with a scaffold N50 of 4.69 Mb and exhibits lower heterozygosity (0.9%) compared to <i>V. villosa</i> Roth (3.1%). Genome analysis revealed significant expansion of long terminal repeat retrotransposons (LTR-RTs), as well as lineage-specific proliferation of miniature inverted-repeat transposable elements (MITEs) in <i>V. villosa</i> var. <i>glabrescens.</i> Comparative genomics with <i>V. villosa</i> Roth highlighted gene family expansions associated with trichome development, providing insights into the genetic basis of morphological and adaptive differences within the <i>Vicia</i> species. This reference genome provides a foundational resource for accelerating the breeding of <i>V. villosa</i> varieties with enhanced agronomic traits and contributes to a broader understanding of legume genomics and plant genome evolution.