Genome Assembly of the Roundjaw Bonefish ( Albula glossodonta ), a Vulnerable Circumtropical Sportfish
Abstract
Background
Bonefishes are cryptic species indiscriminately targeted by subsistence and recreational fisheries worldwide. The roundjaw bonefish, Albula glossodonta is the most widespread bonefish species in the Indo-Pacific and is listed as vulnerable to extinction by the IUCN’s Red List due to anthropogenic activities. Whole-genome datasets allow for improved population and species delimitation, which – prior to this study – were lacking for Albula species.
Results
We generated a high-quality genome assembly of an A. glossodonta individual from Hawai‘i, USA. The assembled contigs had an NG50 of 4.75 Mbp and a maximum length of 28.2 Mbp. Scaffolding yielded an NG50 of 14.49 Mbp, with the longest scaffold reaching 42.29 Mbp. Half the genome was contained in 20 scaffolds. The genome was annotated with 28.3 K protein-coding genes. We then analyzed 66 A. glossodonta individuals and 38,355 SNP loci to evaluate population genetic connectivity between six atolls in Seychelles and Mauritius in the Western Indian Ocean. We observed genetic homogeneity between atolls in Seychelles and evidence of reduced gene flow between Seychelles and Mauritius. The South Equatorial Current could be one mechanism limiting gene flow of A. glossodonta populations between Seychelles and Mauritius.
Conclusions
Quantifying the spatial population structure of widespread fishery species such as bonefishes is necessary for effective transboundary management and conservation. This population genomic dataset mapped to a high-quality genome assembly allowed us to discern shallow population structure in a widespread species in the Western Indian Ocean. The genome assembly will be useful for addressing the taxonomic uncertainties of bonefishes globally.
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This has been published in GigaByte Journal under a CC-BY Open Access license (see https://doi.org/10.46471/gigabyte.44). The open peer reviews have been unpublished under the same license and are as follows:
**Reviewer 1. Changxu Tian ** In this paper, a high-quality genome of the Roundjaw Bonefish was successfully constructed, and population structure for Albula glossodonta or any bonefish species were well investigated with high-resolution genomic data. It serves as a valuable resource for future genomic studies of bonefishes to facilitate their management and conservation. Authors have presented the data in a meaningful way, I recommend the manuscript is publishable upon the following minor concerns are well addressed:
- In the Tissue Collection and Preservation, why not use the same individual sample to complete DNA sequencing, but …
This has been published in GigaByte Journal under a CC-BY Open Access license (see https://doi.org/10.46471/gigabyte.44). The open peer reviews have been unpublished under the same license and are as follows:
**Reviewer 1. Changxu Tian ** In this paper, a high-quality genome of the Roundjaw Bonefish was successfully constructed, and population structure for Albula glossodonta or any bonefish species were well investigated with high-resolution genomic data. It serves as a valuable resource for future genomic studies of bonefishes to facilitate their management and conservation. Authors have presented the data in a meaningful way, I recommend the manuscript is publishable upon the following minor concerns are well addressed:
- In the Tissue Collection and Preservation, why not use the same individual sample to complete DNA sequencing, but use the heart tissue of another individual for long-read sequencing and Hi-C sequencing.
- In the Illumina RNA of Read Error Correction, why use the original read sequenced not filtered?
- In the discussion section, it is suggested to add a discussion on the genomic results of this species.
**Reviewer 2. Shengyong Xu. ** In the present study, the authors reported the genome assembly of bonefish Albula glossodonta, as well as population genomic analyses using ddRAD-seq. These genomic data should be useful for management and conservation of this species. Some comments are as follows. 1. The authors should show us the line numbers in their manuscript.
- In Abstract and Result, the authors should provide fundamental genomic information such as genome size, heterozygosity ratio and repeat ratio, so we can have a better understanding of Albula glossodonta genome.
- Also, the authors should provide the information of final genome assembly of this fish species, i.e. total length of genome assembly, the number and N50 of scaffolds, and among others.
- What’s the meaning of NG50, LG50, and auNG in the manuscript? And what’s the difference between NG50 and N50? The authors should interpret why using these statistical data in the description of genome assembly part.
- With an annotated genome assembly as reference, I suggested the identified SNPs should be annotated using SNPEff or annovar softwares.
- Population genomic approach can uncover population divergence at a fine spatial scale. In this manuscript, relative high levels of genetic differentiation were detected between Mauritius and other three groups based on neutral SNP dataset, suggesting possible local adaptation in Mauritius population. I suggest the authors can further analyze population structure by using outlier dataset to reveal the influence of local adaptation on population differentiation.
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