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

TL;DR

This paper presents a high-quality genome assembly for smooth vetch, a legume cover crop, to support breeding and understanding of legume genomics.

Contribution

The first chromosome-level genome assembly for Vicia villosa var. glabrescens using PacBio HiFi and Hi-C technologies.

Findings

The genome assembly has a scaffold N50 of 4.69 Mb and 96.05% BUSCO completeness.

Significant expansion of LTR-RTs and MITEs was observed in V. villosa var. glabrescens.

Gene family expansions related to trichome development were identified compared to V. villosa Roth.

Abstract

This study has, for the first time, completed the chromosome-level genome assembly of smooth wild pea (Vicia villosa var. glabrescens). This variety is an important leguminous cover crop and has attracted much attention due to its strong nitrogen fixation ability, high biomass, and wide adaptability. By integrating PacBio HiFi long-read sequencing and Hi-C chromatin conformation capture technology, a high-quality genome of 3.70 Gb in size was constructed. This genome has good continuity (with a scaffold N50 of 4.69 Mb), and high completeness (with a BUSCO completeness of 96.05%), and most of the sequences were successfully anchored to seven pseudo-chromosomes. This reference genome (named Vvill-gla1.0) provides an important resource for in-depth analysis of key agronomic traits of Vicia gladiata (such as seed dormancy and stress resistance), will strongly promote its molecular breeding process, and enhance the understanding of genome evolution in leguminous plants.

Vicia villosa Roth var. glabrescens (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 V. villosa var. glabrescens, 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 V. villosa 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 V. villosa var. glabrescens. Comparative genomics with V. villosa Roth highlighted gene family expansions associated with trichome development, providing insights into the genetic basis of morphological and adaptive differences within the Vicia species. This reference genome provides a foundational resource for accelerating the breeding of V. villosa varieties with enhanced agronomic traits and contributes to a broader understanding of legume genomics and plant genome evolution.

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