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. 2022 Jan 31;2022:gigabyte38. doi: 10.46471/gigabyte.38
Reviewer name and names of any other individual's who aided in reviewer Jianbo Jian
Do you understand and agree to our policy of having open and named reviews, and having your review included with the published papers. (If no, please inform the editor that you cannot review this manuscript.) Yes
Is the language of sufficient quality? Yes
Please add additional comments on language quality to clarify if needed
Are all data available and do they match the descriptions in the paper? Yes
Additional Comments
Are the data and metadata consistent with relevant minimum information or reporting standards? See GigaDB checklists for examples <a href="http://gigadb.org/site/guide" target="_blank">http://gigadb.org/site/guide</a> Yes
Additional Comments
Is the data acquisition clear, complete and methodologically sound? Yes
Additional Comments
Is there sufficient detail in the methods and data-processing steps to allow reproduction? Yes
Additional Comments
Is there sufficient data validation and statistical analyses of data quality? Yes
Additional Comments
Is the validation suitable for this type of data? Yes
Additional Comments
Is there sufficient information for others to reuse this dataset or integrate it with other data? Yes
Additional Comments
Any Additional Overall Comments to the Author 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