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

Hangwei Xi,Iain R Searle,Zhipeng Liu,Christopher Ward,Vy Nguyen

doi:10.46471/gigabyte.38

Hangwei Xi, Iain R Searle + Show 3 more

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https://doi.org/10.46471/gigabyte.38

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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 1.65Gbp, with a median contig length of 684Kbp. 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 resource for genomic breeding, genetic diversity and for understanding adaption to diverse arid environments.

Highlights

Vicia sativa L. (Figure 1) is an annual legume belonging to the Fabaceae family, and Vicia genus [1]
No chromosome-level genome assembly has been reported within the Vicia genus
In one drought tolerance study, V. sativa could withstand a month of drought stress, with the leaf weight not decreasing significantly compared with the non-drought control [9]

Summary

Introduction

The 25-mer count distribution data was used as an input to GenomeScope (GenomeScope, RRID:SCR_017014) [20] for genome size estimation with the read length set to 150 and max k-mer coverage set to 1 million. We conducted contig assembly from the Nanopore long-reads using Canu v1.7 (Canu, RRID:SCR_015880) [22] under default parameters with the expected genome size set at 1.77 Gbp. Canu was used to perform read trimming and sequencing error correction for the input data before performing contig assembly. A high fraction of the assembled sequences (93%) were contained in four pseudo-chromosomes (Figure 3A); V. sativa has six pairs of chromosomes [1].

Results

Conclusion