Chromosome-level assembly of the common vetch (Vicia sativa) reference genome

Abstract

Vicia sativa L. (common vetch, n = 6) is an annual, herbaceous, climbing legume, originating in the Fertile Crescent of the Middle East and now widespread in the Mediterranean basin, West, Central and Eastern Asia, North and South America. V. sativa is of economic importance as a forage legume in countries such as Australia, China, and the USA, and contributes valuable nitrogen to agricultural rotation cropping systems. To accelerate precision genome breeding and genomics-based selection of this legume, we present a chromosome-level reference genome sequence for V. sativa, constructed using a combination of long-read Oxford Nanopore sequencing, short-read Illumina sequencing, and high-throughput chromosome conformation data (CHiCAGO and Hi-C) analysis. The chromosome-level assembly of six pseudo-chromosomes has a total genome length of 1.65 Gbp, with a median contig length of 684 Kbp. BUSCO analysis of the assembly demonstrated very high completeness of 98% of the dicotyledonous orthologs.RNA-seq analysis and gene modelling enabled the annotation of 53,218 protein-coding genes. This V. sativa assembly will provide insights into vetch genome evolution and be a valuable

A reference assembly for the legume cover crop, hairy vetch (Vicia villosa)

“…The expected genome size of 2.0 Gbp [20] is much larger, but k-merbased estimations are generally underestimates. The estimated heterozygosity of V. villosa was 3.14% (Figure 2), which was substantially higher than that reported for V. sativa (0.09%) [11].…”

“…Rows with a "PE" suffix indicate features identified by FRCbam [41] and detailed definitions for each can be found in the original publication. a Summary statistics for the V. sativa assembly were taken from [11]. Scaffold assignments (blue boxes) were identified from an optimal arrangement of signal along the diagonal.…”

The giant diploid faba genome unlocks variation in a global protein crop

“…Of note, the agronomically relevant family of leghaemoglobins had expanded (Supplementary Table 7). Despite this, the absence of a lineage-specific WGD or widespread gene family expansion means that the proliferation of repeat elements largely explains why the faba genome is more than seven times larger than that of its close relative common vetch (Vicia sativa) 30 .…”

Volatile profiles of commercial vetch prepared via different processing methods

“…v0.6.7 (Trim Galore, RRID:SCR_011847). High quality reads were then mapped to the V. sativa genome (Xi et al, 2021) using BWA mem v0.7.17 (BWA, RRID:SCR_010910) with default parameters. The mapping result was converted into BAM file format using Samtools v1.13 (SAMTOOLS, RRID:SCR_002105) .…”

“…Phylogenetic analysis was performed to confirm the classification of those varieties used in this study. Whole genome sequencing (WGS) reads of five V. sativa varieties, and four additional Vicia species, V. villosa variety Latigo, V. pannocia, V. ervilla and V. narbonensis were generated and aligned to the V. sativa reference genome (Xi et al, 2021). Single nucleotide polymorphisms (SNPs) were identified and used to determine the genetic relationship amongst the genomes by phylogenetic analysis.…”