Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific
Holacanthus angelfishes are some of the most iconic marine fishes of the Tropical Eastern Pacific (TEP). However, very limited genomic resources currently exist for the genus. In this study we: (i) assembled and annotated the nuclear genome of the King Angelfish (Holacanthus passer), an...
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| Format: | Article |
| Language: | English |
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GigaScience Press
2024-03-01
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| Series: | GigaByte |
| Online Access: | https://gigabytejournal.com/articles/115 |
| _version_ | 1797253752240996352 |
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| author | Remy Gatins Carlos F. Arias Carlos Sánchez Giacomo Bernardi Luis F. De León |
| author_facet | Remy Gatins Carlos F. Arias Carlos Sánchez Giacomo Bernardi Luis F. De León |
| author_sort | Remy Gatins |
| collection | DOAJ |
| description |
Holacanthus angelfishes are some of the most iconic marine fishes of the Tropical Eastern Pacific (TEP). However, very limited genomic resources currently exist for the genus. In this study we: (i) assembled and annotated the nuclear genome of the King Angelfish (Holacanthus passer), and (ii) examined the demographic history of H. passer in the TEP. We generated 43.8 Gb of ONT and 97.3 Gb Illumina reads representing 75× and 167× coverage, respectively. The final genome assembly size was 583 Mb with a contig N50 of 5.7 Mb, which captured 97.5% of the complete Actinoterygii Benchmarking Universal Single-Copy Orthologs (BUSCOs). Repetitive elements accounted for 5.09% of the genome, and 33,889 protein-coding genes were predicted, of which 22,984 were functionally annotated. Our demographic analysis suggests that population expansions of H. passer occurred prior to the last glacial maximum (LGM) and were more likely shaped by events associated with the closure of the Isthmus of Panama. This result is surprising, given that most rapid population expansions in both freshwater and marine organisms have been reported to occur globally after the LGM. Overall, this annotated genome assembly provides a novel molecular resource to study the evolution of Holacanthus angelfishes, while facilitating research into local adaptation, speciation, and introgression in marine fishes.
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| first_indexed | 2024-04-24T21:39:03Z |
| format | Article |
| id | doaj.art-11b5fb18e9454952bc9e7900d73afead |
| institution | Directory Open Access Journal |
| issn | 2709-4715 |
| language | English |
| last_indexed | 2024-04-24T21:39:03Z |
| publishDate | 2024-03-01 |
| publisher | GigaScience Press |
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| spelling | doaj.art-11b5fb18e9454952bc9e7900d73afead2024-03-21T11:23:10ZengGigaScience PressGigaByte2709-47152024-03-0110.46471/gigabyte.115Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern PacificRemy Gatins 0https://orcid.org/0000-0002-1786-9381Carlos F. Arias 1https://orcid.org/0000-0002-1546-5156Carlos Sánchez 2https://orcid.org/0000-0001-7199-1268Giacomo Bernardi 3https://orcid.org/0000-0002-8249-4678Luis F. De León 4https://orcid.org/0000-0001-9317-420XDepartment of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA, Department of Biology, University of Massachusetts, Boston, MA, USA, Marine and Environmental Sciences, Northeastern University, Boston, MA, USADepartment of Biology, University of Massachusetts, Boston, MA, USA, Smithsonian Tropical Research Institute, Panamá, Panama, Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC, USADepartamento de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, CP 23080, La Paz, Baja California Sur, MéxicoDepartment of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USADepartment of Biology, University of Massachusetts, Boston, MA, USA Holacanthus angelfishes are some of the most iconic marine fishes of the Tropical Eastern Pacific (TEP). However, very limited genomic resources currently exist for the genus. In this study we: (i) assembled and annotated the nuclear genome of the King Angelfish (Holacanthus passer), and (ii) examined the demographic history of H. passer in the TEP. We generated 43.8 Gb of ONT and 97.3 Gb Illumina reads representing 75× and 167× coverage, respectively. The final genome assembly size was 583 Mb with a contig N50 of 5.7 Mb, which captured 97.5% of the complete Actinoterygii Benchmarking Universal Single-Copy Orthologs (BUSCOs). Repetitive elements accounted for 5.09% of the genome, and 33,889 protein-coding genes were predicted, of which 22,984 were functionally annotated. Our demographic analysis suggests that population expansions of H. passer occurred prior to the last glacial maximum (LGM) and were more likely shaped by events associated with the closure of the Isthmus of Panama. This result is surprising, given that most rapid population expansions in both freshwater and marine organisms have been reported to occur globally after the LGM. Overall, this annotated genome assembly provides a novel molecular resource to study the evolution of Holacanthus angelfishes, while facilitating research into local adaptation, speciation, and introgression in marine fishes. https://gigabytejournal.com/articles/115 |
| spellingShingle | Remy Gatins Carlos F. Arias Carlos Sánchez Giacomo Bernardi Luis F. De León Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific GigaByte |
| title | Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific |
| title_full | Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific |
| title_fullStr | Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific |
| title_full_unstemmed | Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific |
| title_short | Whole genome assembly and annotation of the King Angelfish (Holacanthus passer) gives insight into the evolution of marine fishes of the Tropical Eastern Pacific |
| title_sort | whole genome assembly and annotation of the king angelfish holacanthus passer gives insight into the evolution of marine fishes of the tropical eastern pacific |
| url | https://gigabytejournal.com/articles/115 |
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