Whole-genome re-sequencing of the Baikal seal and other phocid seals for a glimpse into their genetic diversity, demographic history, and phylogeny
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Editors Assessment:
Due to them being found in the landlocked, isolated habitat of Lake Baikal makes the Baikal Seal (Pusa sibirica) unique among all pinnipeds as the only freshwater seal. This paper presents reference-based assemblies of six newly sequenced Baikal seal individuals, one individual of the ringed seal, as well as the first short-read data of the harbor seal and the Caspian seal . This data aiding the study of the genomic diversity of the Baikal seal and to contribute baseline data to the limited genomic data available for seals. Peer review extended the description of the used tools and parameters in the revised manuscript, and provided some more information on the methods..This newly generated sequencing data hopefully now helps to extend the phylogeny of the Phoca/Pusa group on genome-wide data and can also broaden the view into the genetic structure and diversity of the Baikal seal
This evaluation refers to version 1 of the preprint
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Abstract
The Baikal seal (Pusa sibirica) is a freshwater seal endemic to Lake Baikal, where it became landlocked million years ago. It is an abundant species of least concern despite the limited habitat. Research on its genetic diversity had only been done on mitochondrial genes, restriction fragment analyses, and microsatellites, before its reference genome was published. Here, we report the genome sequences of six Baikal seals, and one individual of the Caspian, ringed, and harbor seal, re-sequenced from Illumina paired-end short read data. Heterozygosity calculations of the six newly sequenced individuals are similar to previously reported genomes. Also, the novel genome data of the other species contributed to a more complete phocid seal phylogeny based on whole-genome data. Despite the isolation of the land-locked Baikal seal, its genetic diversity is comparable to that of other seal species. Future targeted genome studies need to explore the genomic diversity throughout their distribution.
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Editors Assessment:
Due to them being found in the landlocked, isolated habitat of Lake Baikal makes the Baikal Seal (Pusa sibirica) unique among all pinnipeds as the only freshwater seal. This paper presents reference-based assemblies of six newly sequenced Baikal seal individuals, one individual of the ringed seal, as well as the first short-read data of the harbor seal and the Caspian seal . This data aiding the study of the genomic diversity of the Baikal seal and to contribute baseline data to the limited genomic data available for seals. Peer review extended the description of the used tools and parameters in the revised manuscript, and provided some more information on the methods..This newly generated sequencing data hopefully now helps to extend the phylogeny of the Phoca/Pusa group on genome-wide data and can also broaden the …
Editors Assessment:
Due to them being found in the landlocked, isolated habitat of Lake Baikal makes the Baikal Seal (Pusa sibirica) unique among all pinnipeds as the only freshwater seal. This paper presents reference-based assemblies of six newly sequenced Baikal seal individuals, one individual of the ringed seal, as well as the first short-read data of the harbor seal and the Caspian seal . This data aiding the study of the genomic diversity of the Baikal seal and to contribute baseline data to the limited genomic data available for seals. Peer review extended the description of the used tools and parameters in the revised manuscript, and provided some more information on the methods..This newly generated sequencing data hopefully now helps to extend the phylogeny of the Phoca/Pusa group on genome-wide data and can also broaden the view into the genetic structure and diversity of the Baikal seal
This evaluation refers to version 1 of the preprint
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AbstractBackground: The iconic Baikal seal (Pusa sibirica), the smallest true seal, is a freshwater seal that is endemic to Lake Baikal where it became landlocked some million years ago. It is a rather abundant species of least concern, despite the limited habitat. Until recently, research on its genetic diversity has only been done on mitochondrial genes, restriction fragment analyses, and microsatellites, before its reference genome has been published. Findings: Here we report the genome sequences of six Baikal seals, and one individual of the Caspian seal, ringed seal, and the harbor seal, re-sequenced from Illumina paired-end short read data. Heterozygosity calculations of the six newly sequenced individuals are like the previously reported genomes. In addition, the novel genome data of the other species contributed to a more …
AbstractBackground: The iconic Baikal seal (Pusa sibirica), the smallest true seal, is a freshwater seal that is endemic to Lake Baikal where it became landlocked some million years ago. It is a rather abundant species of least concern, despite the limited habitat. Until recently, research on its genetic diversity has only been done on mitochondrial genes, restriction fragment analyses, and microsatellites, before its reference genome has been published. Findings: Here we report the genome sequences of six Baikal seals, and one individual of the Caspian seal, ringed seal, and the harbor seal, re-sequenced from Illumina paired-end short read data. Heterozygosity calculations of the six newly sequenced individuals are like the previously reported genomes. In addition, the novel genome data of the other species contributed to a more complete phocid seal phylogeny based on whole-genome data. Conclusions: Despite the long isolation of the land-locked Baikal seal population, the genetic diversity of this species is in the same range as other seal species. The Baikal seal appears to form a single, diverse population. However, targeted genome studies are needed to explore the genomic diversity throughout their distribution.
This work has been published in GigaByte Journal under a CC-BY 4.0 license (https://doi.org/10.46471/gigabyte.142). These reviews are as follows.
Reviewer 1. Yaolei Zhang
Overall, the newly generated data from this study are valuable, but the authors have not effectively analyzed and interpreted the data. The entire paper appears to be more like an undergraduate bioinformatics homework exercise, with the results resembling a middle school student's description of a picture. Additionally, there are several major issues:
- Background investigation is not sufficient: Genomic data on the Baikal seal has been publicly available five years ago, including a chromosome-level genome assemby with much higher quality, such as contig N50, which is nearly ten times higher than the reference genome used by the author in this study.
- Methodology is unclear: The description of the software and parameters used is incomplete. A proper methodological description should allow a basic bioinformatics analyst to quickly reproduce the results of the paper. However, with the current description, there are too many missing details in the methodology section.
- Data issues: • a. For publicly available data, the authors did not provide detailed descriptions of the accession numbers. • b. For the newly generated data in this study, the author did not sufficiently describe the data quality to support their conclusions. • c. In the supplementary table, the author show 100% mapping rates of sequencing reads for all samples. Having worked on numerous resequencing projects, I have rarely encountered 100% mapping rates, especially when aligning to different species. The author should check this.
- Basic analytical skill/experience is lacking: For example, the PSMC analysis, sequencing depth can directly affect the results, but the author did not consider this issue and proceeded to compare curves generated from different sequencing depths directly. Additionally, how was the mutation rate (μ) derived? The generation time is only mentioned as coming from IUCN, but values are not provided in the paper. Moreover, in the genetic diversity section, is calculating heterozygosity only sufficient to be considered a measure of genetic diversity? Hope the author to read some re-sequencing papers thoroughly Re-review: The authors carefully addressed most of my concerns. Although I still doubt about the mapping rate (I did no find the mapping report attached), I am happy to accept this manuscript.
Reviewer 2. Stephen Gaughran
Are all data available and do they match the descriptions in the paper? Yes. NCBI numbers should be added when available.
Comments: I would recommend using a lower mutation rate for seals: de novo mutation rates around 7e-9 have been measured for a few pinniped species. Line 129: I think you mean kya here (not Ma). Line 160: I think this should be "an average value of 0.066%"
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