Genome assembly of the roundjaw bonefish (Albula glossodonta), a vulnerable circumtropical sportfish
The roundjaw bonefish, Albula glossodonta, is the most widespread albulid in the Indo-Pacific and is vulnerable to extinction. We assembled the genome of a roundjaw bonefish from Hawai‘i, USA, which will be instrumental for effective transboundary management and conservation when paired...
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| Format: | Article |
| Language: | English |
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GigaScience Press
2022-03-01
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| Series: | GigaByte |
| Online Access: | https://gigabytejournal.com/articles/44 |
| _version_ | 1797884359151190016 |
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| author | Brandon D. Pickett Sheena Talma Jessica R. Glass Daniel Ence Timothy P. Johnson Paul D. Cowley Perry G. Ridge John S. K. Kauwe |
| author_facet | Brandon D. Pickett Sheena Talma Jessica R. Glass Daniel Ence Timothy P. Johnson Paul D. Cowley Perry G. Ridge John S. K. Kauwe |
| author_sort | Brandon D. Pickett |
| collection | DOAJ |
| description |
The roundjaw bonefish, Albula glossodonta, is the most widespread albulid in the Indo-Pacific and is vulnerable to extinction. We assembled the genome of a roundjaw bonefish from Hawai‘i, USA, which will be instrumental for effective transboundary management and conservation when paired with population genomics datasets. The 1.05 gigabase pair (Gbp) contig-level assembly had a 4.75 megabase pair (Mbp) NG50 and a maximum contig length of 28.2 Mbp. Scaffolding yielded an LG50 of 20 and an NG50 of 14.49 Mbp, with the longest scaffold reaching 42.29 Mbp. The genome comprised 6.5% repetitive elements and was annotated with 28.3 K protein-coding genes. We then evaluated population genetic connectivity between six atolls in the Western Indian Ocean with 38,355 SNP loci across 66 A. glossodonta individuals. We discerned shallow population structure and observed genetic homogeneity between atolls in Seychelles and reduced gene flow between Seychelles and Mauritius. The South Equatorial Current might be the limiting mechanism of this reduced gene flow. The genome assembly will be useful for addressing taxonomic uncertainties of bonefishes globally.
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| first_indexed | 2024-04-10T04:05:16Z |
| format | Article |
| id | doaj.art-9c26f156365141eca99c75a194d704f7 |
| institution | Directory Open Access Journal |
| issn | 2709-4715 |
| language | English |
| last_indexed | 2024-04-10T04:05:16Z |
| publishDate | 2022-03-01 |
| publisher | GigaScience Press |
| record_format | Article |
| series | GigaByte |
| spelling | doaj.art-9c26f156365141eca99c75a194d704f72023-03-13T06:18:15ZengGigaScience PressGigaByte2709-47152022-03-0110.46471/gigabyte.44Genome assembly of the roundjaw bonefish (Albula glossodonta), a vulnerable circumtropical sportfishBrandon D. Pickett 0https://orcid.org/0000-0001-8235-4440Sheena Talma 1https://orcid.org/0000-0003-2971-6523Jessica R. Glass 2https://orcid.org/0000-0002-9843-1786Daniel Ence 3https://orcid.org/0000-0001-6099-9985Timothy P. Johnson 4https://orcid.org/0000-0002-8323-8414Paul D. Cowley 5https://orcid.org/0000-0003-1246-4390Perry G. Ridge 6https://orcid.org/0000-0001-6944-2753John S. K. Kauwe 7https://orcid.org/0000-0001-8641-2468Department of Biology, Brigham Young University, Provo, Utah, USADepartment of Ichthyology and Fisheries Science, Rhodes University, Makhanda, South AfricaSouth African Institute for Aquatic Biodiversity, Makhanda, South Africa, College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, Alaska, USASchool of Forest Resources and Conservation, University of Florida, Gainesville, Florida, USATim Johnson Gallery, Mesa, Arizona, USASouth African Institute for Aquatic Biodiversity, Makhanda, South AfricaDepartment of Biology, Brigham Young University, Provo, Utah, USADepartment of Biology, Brigham Young University, Provo, Utah, USA, Brigham Young University – Hawai‘i, Laie, Hawai‘i, USA The roundjaw bonefish, Albula glossodonta, is the most widespread albulid in the Indo-Pacific and is vulnerable to extinction. We assembled the genome of a roundjaw bonefish from Hawai‘i, USA, which will be instrumental for effective transboundary management and conservation when paired with population genomics datasets. The 1.05 gigabase pair (Gbp) contig-level assembly had a 4.75 megabase pair (Mbp) NG50 and a maximum contig length of 28.2 Mbp. Scaffolding yielded an LG50 of 20 and an NG50 of 14.49 Mbp, with the longest scaffold reaching 42.29 Mbp. The genome comprised 6.5% repetitive elements and was annotated with 28.3 K protein-coding genes. We then evaluated population genetic connectivity between six atolls in the Western Indian Ocean with 38,355 SNP loci across 66 A. glossodonta individuals. We discerned shallow population structure and observed genetic homogeneity between atolls in Seychelles and reduced gene flow between Seychelles and Mauritius. The South Equatorial Current might be the limiting mechanism of this reduced gene flow. The genome assembly will be useful for addressing taxonomic uncertainties of bonefishes globally. https://gigabytejournal.com/articles/44 |
| spellingShingle | Brandon D. Pickett Sheena Talma Jessica R. Glass Daniel Ence Timothy P. Johnson Paul D. Cowley Perry G. Ridge John S. K. Kauwe Genome assembly of the roundjaw bonefish (Albula glossodonta), a vulnerable circumtropical sportfish GigaByte |
| title | Genome assembly of the roundjaw bonefish (Albula glossodonta), a vulnerable circumtropical sportfish |
| title_full | Genome assembly of the roundjaw bonefish (Albula glossodonta), a vulnerable circumtropical sportfish |
| title_fullStr | Genome assembly of the roundjaw bonefish (Albula glossodonta), a vulnerable circumtropical sportfish |
| title_full_unstemmed | Genome assembly of the roundjaw bonefish (Albula glossodonta), a vulnerable circumtropical sportfish |
| title_short | Genome assembly of the roundjaw bonefish (Albula glossodonta), a vulnerable circumtropical sportfish |
| title_sort | genome assembly of the roundjaw bonefish albula glossodonta a vulnerable circumtropical sportfish |
| url | https://gigabytejournal.com/articles/44 |
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