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Chromosome‑level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus

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Title Chromosome‑level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus
 
Creator Etherington, Graham J.
Nash, Will
Ciezarek, Adam
Mehta, Tarang
Barria, Agustin
Penaloza, Carolina
Khan, M.G.Q.
Durrant, Alex
Forres, Nicole
Fraser, Fiona
Irish, Naomi
Kaithakottil, Gemy
Lipscombe, James
Trịnh Quốc Trọng
Watkins, Chris
Swarbreck, David
Angiolini, Emily
Cnaani, Avner
Gharbi, Karim
Houston, Ross
Benzie, John A.H.
Haerty, Wilfried
 
Subject aquaculture
introgression
tilapia
Fish
reference genome
 
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.
 
Date 2022-12-15
2023-01-10T16:36:27Z
2023-01-10T16:36:27Z
 
Type Journal Article
 
Identifier 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).
1471-2164
https://hdl.handle.net/10568/126756
https://doi.org/10.1186/s12864-022-09065-8
 
Language en
 
Rights CC-BY-4.0
Open Access
 
Format application/pdf
 
Publisher Springer Science and Business Media LLC
 
Source BMC Genomics