Reconstruction of the X and Y haplotypes in the genetically improved Abbassa nile tilapia genome assembly
The success of the Nile tilapia (Oreochromis niloticus) as an aquaculture species is partly the result of continuous selective breeding leading to high performing strains. These elite strains have been derived from breeding populations of diverse origins and crosses with other Oreochromis species. O...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
nature portfolio
2025
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/177765 |
| _version_ | 1855527598111588352 |
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| author | Etherington, Graham Ciezarek, Adam Mehta, T Barker, T Durrant, Alex Fraser, Fiona Henderson, S Irish, Naomi Kaithakottil, Gemy Knitlhoffer, V Ali, Shimaa Trinh, Trong Watkins, Chris Swarbreck, David Gharbi, Karim Benzie, John Haerty, Wilfried |
| author_browse | Ali, Shimaa Barker, T Benzie, John Ciezarek, Adam Durrant, Alex Etherington, Graham Fraser, Fiona Gharbi, Karim Haerty, Wilfried Henderson, S Irish, Naomi Kaithakottil, Gemy Knitlhoffer, V Mehta, T Swarbreck, David Trinh, Trong Watkins, Chris |
| author_facet | Etherington, Graham Ciezarek, Adam Mehta, T Barker, T Durrant, Alex Fraser, Fiona Henderson, S Irish, Naomi Kaithakottil, Gemy Knitlhoffer, V Ali, Shimaa Trinh, Trong Watkins, Chris Swarbreck, David Gharbi, Karim Benzie, John Haerty, Wilfried |
| author_sort | Etherington, Graham |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | The success of the Nile tilapia (Oreochromis niloticus) as an aquaculture species is partly the result of continuous selective breeding leading to high performing strains. These elite strains have been derived from breeding populations of diverse origins and crosses with other Oreochromis species. Owing to the complex and unique evolutionary histories of each strain, existing reference genomes of wild populations are unsuitable to implement genomic selection for beneficial traits such as growth or environmental resilience in aquaculture programmes. Here we generated a high-quality genome assembly and annotation of the WorldFish Genetically Improved Abbassa Nile tilapia (GIANT) elite strain using a combination of PacBio HiFi, and Omni-C Illumina sequencing. As a male Abbassa Nile tilapia was used for the generation of the genome assembly, we reconstructed both X and Y haplotypes, identifying both amhY and amhΔy on LG23 indicating that Abbassa likely shares the same sex determination system as GIFT, and thereby differs from the existing reference genome, whose sex determination loci are located on LG1. |
| format | Journal Article |
| id | CGSpace177765 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | nature portfolio |
| publisherStr | nature portfolio |
| record_format | dspace |
| spelling | CGSpace1777652025-12-18T02:09:11Z Reconstruction of the X and Y haplotypes in the genetically improved Abbassa nile tilapia genome assembly Etherington, Graham Ciezarek, Adam Mehta, T Barker, T Durrant, Alex Fraser, Fiona Henderson, S Irish, Naomi Kaithakottil, Gemy Knitlhoffer, V Ali, Shimaa Trinh, Trong Watkins, Chris Swarbreck, David Gharbi, Karim Benzie, John Haerty, Wilfried introgression sex determination oreochromis niloticus nile tilapia fish genome assembly abbassa The success of the Nile tilapia (Oreochromis niloticus) as an aquaculture species is partly the result of continuous selective breeding leading to high performing strains. These elite strains have been derived from breeding populations of diverse origins and crosses with other Oreochromis species. Owing to the complex and unique evolutionary histories of each strain, existing reference genomes of wild populations are unsuitable to implement genomic selection for beneficial traits such as growth or environmental resilience in aquaculture programmes. Here we generated a high-quality genome assembly and annotation of the WorldFish Genetically Improved Abbassa Nile tilapia (GIANT) elite strain using a combination of PacBio HiFi, and Omni-C Illumina sequencing. As a male Abbassa Nile tilapia was used for the generation of the genome assembly, we reconstructed both X and Y haplotypes, identifying both amhY and amhΔy on LG23 indicating that Abbassa likely shares the same sex determination system as GIFT, and thereby differs from the existing reference genome, whose sex determination loci are located on LG1. 2025-05-08 2025-11-11T05:42:21Z 2025-11-11T05:42:21Z Journal Article https://hdl.handle.net/10568/177765 en Open Access application/pdf nature portfolio Etherington, G. Ciezarek, A. Mehta, T. Barker, T. Durrant, A. Fraser, F. Henderson, S. Irish, N. Kaithakottil, G. Knitlhoffer, V. Ali, S. Trong, T. Watkins, C. Swarbreck, D. Gharbi, K. Benzie, J. Haerty, W. 2025. Reconstruction of the X and Y haplotypes in the genetically improved Abbassa Nile tilapia genome assembly. Scientific Reports 15, 16057. https://doi.org/10.1038/s41598-025-01300-y |
| spellingShingle | introgression sex determination oreochromis niloticus nile tilapia fish genome assembly abbassa Etherington, Graham Ciezarek, Adam Mehta, T Barker, T Durrant, Alex Fraser, Fiona Henderson, S Irish, Naomi Kaithakottil, Gemy Knitlhoffer, V Ali, Shimaa Trinh, Trong Watkins, Chris Swarbreck, David Gharbi, Karim Benzie, John Haerty, Wilfried Reconstruction of the X and Y haplotypes in the genetically improved Abbassa nile tilapia genome assembly |
| title | Reconstruction of the X and Y haplotypes in the genetically improved Abbassa nile tilapia genome assembly |
| title_full | Reconstruction of the X and Y haplotypes in the genetically improved Abbassa nile tilapia genome assembly |
| title_fullStr | Reconstruction of the X and Y haplotypes in the genetically improved Abbassa nile tilapia genome assembly |
| title_full_unstemmed | Reconstruction of the X and Y haplotypes in the genetically improved Abbassa nile tilapia genome assembly |
| title_short | Reconstruction of the X and Y haplotypes in the genetically improved Abbassa nile tilapia genome assembly |
| title_sort | reconstruction of the x and y haplotypes in the genetically improved abbassa nile tilapia genome assembly |
| topic | introgression sex determination oreochromis niloticus nile tilapia fish genome assembly abbassa |
| url | https://hdl.handle.net/10568/177765 |
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