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

  1. Hangwei Xi
  2. Vy Nguyen
  3. Christopher Ward
  4. Zhipeng Liu
  5. Iain R. Searle

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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 1.65 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 resource for genomic breeding, genetic diversity and for understanding adaption to diverse arid environments.

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  1. GigaByte

    Background

    **Reviewer 2. Jianbo Jian ** In this manuscript, Xi et al reported a chromosome-level genome of the common vetch (Vicia sativa) with integration of Oxford Nanopore sequencing, Illumina sequencing, CHiCAGO and Hi-C. Then, the gene annotation and evolution were performed based on the reference genomes. These genomic resources are valuable for evolution research, genetic diversity and genomic breeding. I think this manuscript is suitable published in Gigabyte. Some minor comments and suggestions as following:

    1. The Line Number is missed in this manuscript, which make the detailed comments is not inconvenient.
    2. Page 6, “resequenced short-reads” should be “De novo sequencing” or “sequencing”.
    3. For the 1.93 Gb assembled genome size, it is a little larger than that of estimated by the flow cytometry (1.77 Gb) and Genomescope (1.61 Gb). Maybe there are some duplicated sequences in this version of assembled genomes. Some redundancy removal software can deal with this question such as Haplotigs, Purge_dups and so on.
    4. For the evaluation of genome, LTR Assembly Index (LAI) was suggested for the quality assessment.
    5. In Table S2, the mapping rate is very well but the genome coverage is just 76% which looks a little low. What’s the reason?
    6. In Table S4, the gene set was combined by August. However, in methods, the annotation software is BRAKER v2.1.6.

    Recommendation Minor Revision

    Re-review: The revised manuscript and response are satisfactory. The additional analyses that the authors have performed are correctly structured. The data presented is clear. In my opinion, I recommend accepting this manuscript.

  2. GigaByte

    Abstract

    This paper has been published in GigaByte Journal under a CC-BY 4.0 Open Access license (see: https://doi.org/10.46471/gigabyte.38), and the open peer reviews have also been shared under this license. These reviews were as follows.

    **Reviewer 1. Jonathan Kreplak ** Is there sufficient detail in the methods and data-processing steps to allow reproduction?

    No. For "Phylogenetic tree construction and divergence time estimation", 64 single copy orthologs are selected, they should be included in a supplementary table to be able to fully reproduce the analysis. Also, Supplementary table S9 should be related to fossil calibrations but show the length of chromosome.

    Recommendation: Minor revision

  3. Version published to 10.46471/gigabyte.38
  4. Version published to 10.1101/2021.10.11.464017v1 on bioRxiv