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

Abstract

Background: Vicia sativa L. (Common Vetch, n = 6) is an annual, herbaceous, climbing legume that is distributed in tropical, sub-tropical and temperate climates. Originating in the Fertile Crescent of the Middle East, V. sativa is now widespread and grows 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 here present a chromosome-level reference genome sequence for V. sativa. Results: We applied a combination of long-read Oxford Nanopore sequencing, short-read Illumina sequencing, and high-throughput chromosome conformation data (CHiCAGO and Hi-C) analysis to construct a chromosome-level genome of V. sativa. The chromosome-level assembly of six pseudo-chromosomes has a total genome length of 1.9 gigabases (Gb) with a median contig length of 684 kb. Benchmarking Universal Single-Copy Orthologs (BUSCO) of the assembly demonstrated a very high completeness of 98 % of the dicotyledonous orthologs. RNA-seq analysis and gene modelling enabled the annotation of 58,415 protein-coding genes. Conclusions: The high-quality chromosome-level genome assembly of V. sativa will provide novel insights into vetch genome evolution and be a valuable resource for genomic breeding, genetic diversity and for understanding adaption to diverse arid environments.

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

“…To estimate divergence times between V. sativa and other important legume species (Table 10 ), coding sequences of 64 randomly selected single copy orthologs (see Supplementary File 1 [ 57 ] ) were aligned using MACSE v1.2 [ 58 ] . Low-quality regions of each alignment were trimmed using Trimal v1.4.1 (trimAl, RRID: SCR_017334 ) [ 59 ] , resulting in high-quality alignments amounting to 139,956 bp.…”

“…Final assembly and original Nanopore assembly, as well as annotation files, Supplementary File 1, predicted transcript and protein sequences, and bioinformatics supporting information, were deposited in the database GigaDB [ 57 ] . Additionally, assembly, Illumina and Nanopore subreads, and transcriptome raw data are available at NCBI and can be accessed with BioProject PRJNA762450 and BioSample SAMN21393724 .…”

“…Illumina and Nanopore subreads can be obtained, with SRR16004114 and SRR16004115 ; and RNA-sequencing raw reads, as follows: SAMN21545804 , SAMN21545805 , SAMN21545806 , SAMN21545807 and SAMN21545808 . Additional data is available in the GigaScience GigaDB database [ 57 ] . …”