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Etherington, G. J., Nash, W., Ciezarek, A., Mehta, T. K., Barria, A., Peñaloza, C., Khan, M. G. Q., Durrant, A., Forrester, N., Fraser, F., Irish, N., Kaithakottil, G. G., Lipscombe, J., Trong, T., Watkins, C., Swarbreck, D., Angiolini, E., Cnaani, A., Gharbi, K., Houston, R. D., Benzie, J. A. H. and Haerty, W. 
ORCID: https://orcid.org/0000-0003-0111-191X
(2022)
Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus.
BMC Genomics, 23.
ISSN 1471-2164
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Abstract
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.
| Item Type: | Article |
|---|---|
| Additional Information: | Availability of data and materials: All sequencing data generated for the GIFT assembly, along with the final linkage group assembly can be found under ENA study accession PRJEB48957. All scripts are available on the github repository: https://github.com/ethering/gift_assembly_paper. Funding Information: The investigations were supported by the Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation; this research was funded by the BBSRC Core Strategic Programme Grant BB/CSP1720/1 (WH, GJE, WN, AC, TM) and its constituent work packages (BBS/E/T/000PR9818 and BBS/E/T/000PR9819), and the Core Capability Grant BB/CCG1720/1 and the National Capability at the Earlham Institute BBS/E/T/000PR9816 (NC1 - Supporting EI’s ISPs and the UK Community with Genomics and Single Cell Analysis, AD, FF, NI, GGK, JL, CW, DS, KG), BBS/E/T/000PR9811 (NC4 - Enabling and Advancing Life Scientists in data-driven research through Advanced Genomics and Computational Training, NF, EA), and BBS/E/T/000PR9814 (NC 3 - Development and deployment of versatile digital platforms for ‘omics-based data sharing and analysis). |
| Uncontrolled Keywords: | aquaculture,introgression,reference genome,tilapia,biotechnology,genetics ,/dk/atira/pure/subjectarea/asjc/1300/1305 |
| Faculty \ School: | Faculty of Science > School of Biological Sciences Faculty of Science > School of Environmental Sciences |
| UEA Research Groups: | Faculty of Medicine and Health Sciences > Research Centres > Norwich Institute for Healthy Aging |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 25 Oct 2024 11:30 |
| Last Modified: | 01 Nov 2024 13:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97212 |
| DOI: | 10.1186/s12864-022-09065-8 |
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