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

Editors Assessment:

The hairy vetch Vicia villosa is an annual legume widely used as a cover crop due to its ability to withstand harsh winters. Here a new a 2.03GB reference-quality genome is presented, assembled from PacBio HiFi long-sequence reads and Hi-C scaffolding. After adding some more methodological details and long-terminal repeat (LTR) assembly index (LAI) analysis the assembly quality and metrics look quite convincing as a chromosome-scale assembly. This resource hopefully providing the foundation for a genetic improvement program for this important cover crop and forage species.

This evaluation refers to version 1 of the preprint

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ABSTRACTVicia villosa is an incompletely domesticated annual legume of the Fabaceae family native to Europe and Western Asia. V. villosa is widely used as a cover crop and as a forage due to its ability to withstand harsh winters. A reference-quality genome assembly (Vvill1.0) was prepared from low error rate long sequence reads to improve genetic-based trait selection of this species. The Vvill1.0 assembly includes seven scaffolds corresponding to the seven estimated linkage groups and comprising approximately 68% of the total genome size of 2.03 gigabase pairs (Gbp). This assembly is expected to be a useful resource for genetic improvement of this emerging cover crop species as well as to provide useful insights into plant genome evolution.

This work has been published in GigaByte Journal under a CC-BY 4.0 license (https://doi.org/10.46471/gigabyte.98), and has published the reviews under the same license. These are as follows.

Reviewer 1. Rong Liu

See reviewer comments document: https://gigabyte-review.rivervalleytechnologies.com/journal/gx/download-files?YXJ0aWNsZT0zODcmZmlsZT0xNTAmdHlwZT1nZW5lcmljJnZpZXc9ZmFsc2U~

Reiewer 2. Haifei Hu

Fuller et al. conducted an interesting work on the Vicia villosa genome study, which could be beneficial for the science community. However, there are some concerns about this work before it can be published.

Introduction The MS seems to indicate the V.villosa genome is important for breeding, and it is an ideal legume that can grow in winter. But the coming analysis and results are missing to address this. The authors should include additional analysis, at least in the gene annotation session, to indicate what genes are potentially associated with the improvement of genetic-based selection and the ability to grow in winter conditions. After reading the MS, it looks like it mainly focuses on the comparison of the V.vilsoa genome and the V.sativa genome. Please indicate why it is important to do so and provide more background on V.sativa in the introduction. Line 59. It is too sudden to start to describe high heterozygosity as still in the challenge without directly linking to V.villosa. The authors need to include the background that V.villosa is heterozygous first, then talk about how challenging it is to generate an assembly.
Methods Line 112: Why is the estimation based on K-mer size quite different from the generated assembly size? The authors’ explanation is weak and needs an in-depth and better explanation of these unexpected results. Did you see any similar observations in other studies? Please give examples(citations). Line 121: Any reason not to use the commonly used HiFi assembler HFi-asm? Line 142-143: Did you have a file to record which genome regions you have introduced the breaks and how this step was performed? Line 158: the unit bp changed into Mb for better comparison Line 160: Here, you should use contig N50 rather than scaffold N50 to indicate the quality of the gnome. And you need to compare the contig N50 with the V.sativa.
DATA VALIDATION AND QUALITY CONTROL Should perform BUSCO and LAI to assess the quality of the genome in the main text.

4 Phylogenetic tree construction Soybean is an important legume species, and it will make this result more useful and interesting for readers. You should include the Wm82 V4 genome for this analysis. And the version of other legume species’ genomes needs to be indicated.

5 Figures Figure 3 HiC alignment map shows near 600Mb genomes can not be scaffolded into a genome. Any reason? What is the green dot point in the figure? Figure 4 b, the BUSCO of Vvil1.0 is much higher than V.stativa. Any reason? And no description of how you perform the BUSCO analysis in the main text. Figure 6 Circle plot, would that possible to rename the scaffold as a chromosome based on the alignment between V.sativa and V.vil?

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

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