Chromosome‑level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus
Background The Nile tilapia (Oreochromis niloticus) is the third most important freshwater fish for aquaculture. Its success is directly linked to continuous breeding efforts focusing on production traits such as growth rate and weight. Among those elite strains, the Genetically Improved Farmed Tila...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
BioMed Central
2022
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/126756 |
| _version_ | 1855542594433449984 |
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| author | Etherington, Graham Nash, Will Ciezarek, Adam Mehta, Tarang Barria, Agustin Penaloza, Carolina Khan, MGQ Durrant, Alex Forres, Nicole Fraser, Fiona Irish, Naomi Kaithakottil, Gemy Lipscombe, James Trinh, Trong Watkins, Chris Swarbreck, David Angiolini, Emily Cnaani, Avner Gharbi, Karim Houston, Ross Benzie, John Haerty, Wilfried |
| author_browse | Angiolini, Emily Barria, Agustin Benzie, John Ciezarek, Adam Cnaani, Avner Durrant, Alex Etherington, Graham Forres, Nicole Fraser, Fiona Gharbi, Karim Haerty, Wilfried Houston, Ross Irish, Naomi Kaithakottil, Gemy Khan, MGQ Lipscombe, James Mehta, Tarang Nash, Will Penaloza, Carolina Swarbreck, David Trinh, Trong Watkins, Chris |
| author_facet | Etherington, Graham Nash, Will Ciezarek, Adam Mehta, Tarang Barria, Agustin Penaloza, Carolina Khan, MGQ Durrant, Alex Forres, Nicole Fraser, Fiona Irish, Naomi Kaithakottil, Gemy Lipscombe, James Trinh, Trong Watkins, Chris Swarbreck, David Angiolini, Emily Cnaani, Avner Gharbi, Karim Houston, Ross Benzie, John Haerty, Wilfried |
| author_sort | Etherington, Graham |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Background
The Nile tilapia (Oreochromis niloticus) is the third most important freshwater fish for aquaculture. Its success is directly linked to continuous breeding efforts focusing on production traits such as growth rate and weight. Among those elite strains, the Genetically Improved Farmed Tilapia (GIFT) programme initiated by WorldFish is now distributed worldwide. To accelerate the development of the GIFT strain through genomic selection, a high-quality reference genome is necessary.
Results
Using a combination of short (10X Genomics) and long read (PacBio HiFi, PacBio CLR) sequencing and a genetic map for the GIFT strain, we generated a chromosome level genome assembly for the GIFT. Using genomes of two closely related species (O. mossambicus, O. aureus), we characterised the extent of introgression between these species and O. niloticus that has occurred during the breeding process. Over 11 Mb of O. mossambicus genomic material could be identified within the GIFT genome, including genes associated with immunity but also with traits of interest such as growth rate.
Conclusion
Because of the breeding history of elite strains, current reference genomes might not be the most suitable to support further studies into the GIFT strain. We generated a chromosome level assembly of the GIFT strain, characterising its mixed origins, and the potential contributions of introgressed regions to selected traits. |
| format | Journal Article |
| id | CGSpace126756 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | BioMed Central |
| publisherStr | BioMed Central |
| record_format | dspace |
| spelling | CGSpace1267562025-12-08T09:54:28Z Chromosome‑level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus Etherington, Graham Nash, Will Ciezarek, Adam Mehta, Tarang Barria, Agustin Penaloza, Carolina Khan, MGQ Durrant, Alex Forres, Nicole Fraser, Fiona Irish, Naomi Kaithakottil, Gemy Lipscombe, James Trinh, Trong Watkins, Chris Swarbreck, David Angiolini, Emily Cnaani, Avner Gharbi, Karim Houston, Ross Benzie, John Haerty, Wilfried aquaculture introgression tilapia fish reference genome Background The Nile tilapia (Oreochromis niloticus) is the third most important freshwater fish for aquaculture. Its success is directly linked to continuous breeding efforts focusing on production traits such as growth rate and weight. Among those elite strains, the Genetically Improved Farmed Tilapia (GIFT) programme initiated by WorldFish is now distributed worldwide. To accelerate the development of the GIFT strain through genomic selection, a high-quality reference genome is necessary. Results Using a combination of short (10X Genomics) and long read (PacBio HiFi, PacBio CLR) sequencing and a genetic map for the GIFT strain, we generated a chromosome level genome assembly for the GIFT. Using genomes of two closely related species (O. mossambicus, O. aureus), we characterised the extent of introgression between these species and O. niloticus that has occurred during the breeding process. Over 11 Mb of O. mossambicus genomic material could be identified within the GIFT genome, including genes associated with immunity but also with traits of interest such as growth rate. Conclusion Because of the breeding history of elite strains, current reference genomes might not be the most suitable to support further studies into the GIFT strain. We generated a chromosome level assembly of the GIFT strain, characterising its mixed origins, and the potential contributions of introgressed regions to selected traits. 2022-12-15 2023-01-10T16:36:27Z 2023-01-10T16:36:27Z Journal Article https://hdl.handle.net/10568/126756 en Open Access application/pdf BioMed Central Graham Etherington, Will Nash, Adam Ciezarek, Tarang Mehta, Agustin Barria, Carolina Penaloza, MGQ Khan, Alex Durrant, Nicole Forres, Fiona Fraser, Naomi Irish, Gemy Kaithakottil, James Lipscombe, Trong Trinh, Chris Watkins, David Swarbreck, Emily Angiolini, Avner Cnaani, Karim Gharbi, Ross Houston, John Benzie, Wilfried Haerty. (15/12/2022). Chromosome‑level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus. BMC Genomics (23). |
| spellingShingle | aquaculture introgression tilapia fish reference genome Etherington, Graham Nash, Will Ciezarek, Adam Mehta, Tarang Barria, Agustin Penaloza, Carolina Khan, MGQ Durrant, Alex Forres, Nicole Fraser, Fiona Irish, Naomi Kaithakottil, Gemy Lipscombe, James Trinh, Trong Watkins, Chris Swarbreck, David Angiolini, Emily Cnaani, Avner Gharbi, Karim Houston, Ross Benzie, John Haerty, Wilfried Chromosome‑level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus |
| title | Chromosome‑level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus |
| title_full | Chromosome‑level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus |
| title_fullStr | Chromosome‑level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus |
| title_full_unstemmed | Chromosome‑level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus |
| title_short | Chromosome‑level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus |
| title_sort | chromosome level genome sequence of the genetically improved farmed tilapia gift oreochromis niloticus highlights regions of introgression with o mossambicus |
| topic | aquaculture introgression tilapia fish reference genome |
| url | https://hdl.handle.net/10568/126756 |
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