Chromosome-level genome assembly of the common chiton, Liolophura japonica (Lischke, 1873)
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Curated by GigaByte
Editors Assessment:
This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example assembles the genome of the common chiton, Liolophura japonica (Lischke, 1873). Chitons are marine molluscs that can be found worldwide from cold waters to the tropics that play important ecological roles in the environment, but to date are lacking in genomes with only a few assemblies available. This data was produced using PacBio HiFi reads and Omni-C sequencing data, the resulting genome assembly being around 609 Mb in size. From this 28,010 protein-coding genes were predicted. After review improved the methodological details the quality metrics look near chromosome-level, having a scaffold N50 length of 37.34 Mb and 96.1% BUSCO score. This high-quality genome should hopefully be a valuable resource for gaining new insights into the environmental adaptations of L. japonica in residing the intertidal zones and for future investigations in the evolutionary biology in Polyplacophorans and other molluscs.
This evaluation refers to version 1 of the preprint
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Abstract
Chitons (Polyplacophora) are marine molluscs that can be found worldwide from cold waters to the tropics, and play important ecological roles in the environment. Nevertheless, there remains only two chiton genomes sequenced to date. The chiton Liolophura japonica (Lischke, 1873) is one of the most abundant polyplacophorans found throughout East Asia. Our PacBio HiFi reads and Omni-C sequencing data resulted in a high-quality near chromosome-level genome assembly of ∼609 Mb with a scaffold N50 length of 37.34 Mb (96.1% BUSCO). A total of 28,233 genes were predicted, including 28,010 protein-coding genes. The repeat content (27.89%) was similar to the other Chitonidae species and approximately three times lower than in the genome of the Hanleyidae chiton. The genomic resources provided in this work will help to expand our understanding of the evolution of molluscs and the ecological adaptation of chitons.
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Editors Assessment:
This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example assembles the genome of the common chiton, Liolophura japonica (Lischke, 1873). Chitons are marine molluscs that can be found worldwide from cold waters to the tropics that play important ecological roles in the environment, but to date are lacking in genomes with only a few assemblies available. This data was produced using PacBio HiFi reads and Omni-C sequencing data, the resulting genome assembly being around 609 Mb in size. From this 28,010 protein-coding genes were predicted. After review improved the methodological details the quality metrics look near chromosome-level, having a scaffold N50 length of 37.34 Mb and 96.1% BUSCO score. This high-quality …
Editors Assessment:
This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example assembles the genome of the common chiton, Liolophura japonica (Lischke, 1873). Chitons are marine molluscs that can be found worldwide from cold waters to the tropics that play important ecological roles in the environment, but to date are lacking in genomes with only a few assemblies available. This data was produced using PacBio HiFi reads and Omni-C sequencing data, the resulting genome assembly being around 609 Mb in size. From this 28,010 protein-coding genes were predicted. After review improved the methodological details the quality metrics look near chromosome-level, having a scaffold N50 length of 37.34 Mb and 96.1% BUSCO score. This high-quality genome should hopefully be a valuable resource for gaining new insights into the environmental adaptations of L. japonica in residing the intertidal zones and for future investigations in the evolutionary biology in Polyplacophorans and other molluscs.
This evaluation refers to version 1 of the preprint
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AbstractChitons (Polyplacophora) are marine molluscs that can be found worldwide from cold waters to the tropics, and play important ecological roles in the environment. Nevertheless, there remains only two chiton genomes sequenced to date. The chiton Liolophura japonica (Lischke, 1873) is one of the most abundant polyplacophorans found throughout East Asia. Our PacBio HiFi reads and Omni-C sequencing data resulted in a high-quality near chromosome-level genome assembly of ∼609 Mb with a scaffold N50 length of 37.34 Mb (96.1% BUSCO). A total of 28,233 genes were predicted, including 28,010 protein-coding genes. The repeat content (27.89%) was similar to the other Chitonidae species and approximately three times lower than in the genome of the Hanleyidae chiton. The genomic resources provided in this work will help to expand our …
AbstractChitons (Polyplacophora) are marine molluscs that can be found worldwide from cold waters to the tropics, and play important ecological roles in the environment. Nevertheless, there remains only two chiton genomes sequenced to date. The chiton Liolophura japonica (Lischke, 1873) is one of the most abundant polyplacophorans found throughout East Asia. Our PacBio HiFi reads and Omni-C sequencing data resulted in a high-quality near chromosome-level genome assembly of ∼609 Mb with a scaffold N50 length of 37.34 Mb (96.1% BUSCO). A total of 28,233 genes were predicted, including 28,010 protein-coding genes. The repeat content (27.89%) was similar to the other Chitonidae species and approximately three times lower than in the genome of the Hanleyidae chiton. The genomic resources provided in this work will help to expand our understanding of the evolution of molluscs and the ecological adaptation of chitons.
This work has been published in GigaByte Journal under a CC-BY 4.0 license (https://doi.org/10.46471/gigabyte.123), and has published the reviews under the same license. This is part of a thematic series presenting Data Releases from the Hong Kong Biodiversity Genomics consortium (https://doi.org/10.46471/GIGABYTE_SERIES_0006). These are as follows.
Reviewer 1. Jin Sun
Are all data available and do they match the descriptions in the paper?
Yes. The assembly and annotations can be found in the Figshare.
Is the validation suitable for this type of data?
Yes. I have examined the HiC interaction map, and I think the scaffolding is high-quality.
Additional Comments:
The presentation is clear, but I would suggest the authors include the latest BUSCO score for the gene models.
Reviewer 2. Priscila M Salloum
Is the language of sufficient quality?
Yes. The language is appropriate and does not hinder understanding, but some minor proof reading could benefit the manuscript. I left a few suggestions in my comments to the authors.
Are all data available and do they match the descriptions in the paper?
No. The data made available on NCBI has the 632 scaffolds, but the 13 pseudomolecules are not shown (in GCA_032854445.1, under Chromosomes, it reads “This scaffold-level genome assembly includes 632 scaffolds and no assembled chromosomes”), please clarify where information/data for the 13 pseudomolecules can be found. The figshare repository has the annotation files, but it lacks a metadata file detailing what each of the annotation files is (the file names are descriptive, but they do not replace a metadata file). The data availability statement lacks information about the transcriptomes (were these made available?) Supplementary tables are mentioned in the text file but were not made available (at least not for review).
Are the data and metadata consistent with relevant minimum information or reporting standards?
Yes. All that was provided was consistent.
Is the data acquisition clear, complete and methodologically sound?
No. Some clarification is needed (was the same sample used for the genome and transcriptome assembly? Were the different tissues processed in the same way? What software were used for all the bioinformatics steps? What were all the parameters and filters used for genome and transcriptome assembly and annotation?) I left specific suggestions in a file with additional comments to the authors.
Is there sufficient detail in the methods and data-processing steps to allow reproduction?
No. Software versions, citations, and parameters are missing from the methods section. Some results refer to methods not explained in the methods section.
Is the validation suitable for this type of data?
Yes. More details on the BlobTools parameters used are needed.
Is there sufficient information for others to reuse this dataset or integrate it with other data?
No. Supplementary tables were mentioned but not provided (at least not for review). There is enough information for others to reuse the genome data, although more information in the methods section (as mentioned above) and a metadata file would make this even more useful. There is no mention of where the transcriptome has been deposited, and an extremely brief mention to how it was assembled (e.g., no details on parameters used or software versions).
Additional Comments: Please include all citations in the reference list.
And see additional file with comments: https://gigabyte-review.rivervalleytechnologies.com/journal/gx/download-files?YXJ0aWNsZV9pZD00OTYmZmlsZT0xOTgmdHlwZT1nZW5lcmljJnZpZXc9dHJ1ZQ==
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