Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus
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 Fa...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2022-12-01
|
| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-022-09065-8 |
| _version_ | 1798005171452641280 |
|---|---|
| author | G. J. Etherington W. Nash A. Ciezarek T. K. Mehta A. Barria C. Peñaloza M. G. Q. Khan A. Durrant N. Forrester F. Fraser N. Irish G. G. Kaithakottil J. Lipscombe T. Trong C. Watkins D. Swarbreck E. Angiolini A. Cnaani K. Gharbi R. D. Houston J. A. H. Benzie W. Haerty |
| author_facet | G. J. Etherington W. Nash A. Ciezarek T. K. Mehta A. Barria C. Peñaloza M. G. Q. Khan A. Durrant N. Forrester F. Fraser N. Irish G. G. Kaithakottil J. Lipscombe T. Trong C. Watkins D. Swarbreck E. Angiolini A. Cnaani K. Gharbi R. D. Houston J. A. H. Benzie W. Haerty |
| author_sort | G. J. Etherington |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-11T12:36:00Z |
| format | Article |
| id | doaj.art-cb164b73212240a292a50ca50aa43b4b |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-11T12:36:00Z |
| publishDate | 2022-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-cb164b73212240a292a50ca50aa43b4b2022-12-22T04:23:38ZengBMCBMC Genomics1471-21642022-12-0123111610.1186/s12864-022-09065-8Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicusG. J. Etherington0W. Nash1A. Ciezarek2T. K. Mehta3A. Barria4C. Peñaloza5M. G. Q. Khan6A. Durrant7N. Forrester8F. Fraser9N. Irish10G. G. Kaithakottil11J. Lipscombe12T. Trong13C. Watkins14D. Swarbreck15E. Angiolini16A. Cnaani17K. Gharbi18R. D. Houston19J. A. H. Benzie20W. Haerty21Earlham Institute, Norwich Research ParkEarlham Institute, Norwich Research ParkEarlham Institute, Norwich Research ParkEarlham Institute, Norwich Research ParkThe Roslin Institute, The University of EdinburghThe Roslin Institute, The University of EdinburghThe Roslin Institute, The University of EdinburghEarlham Institute, Norwich Research ParkEarlham Institute, Norwich Research ParkEarlham Institute, Norwich Research ParkEarlham Institute, Norwich Research ParkEarlham Institute, Norwich Research ParkEarlham Institute, Norwich Research ParkWorldFishEarlham Institute, Norwich Research ParkEarlham Institute, Norwich Research ParkEarlham Institute, Norwich Research ParkDepartment of Poultry and Aquaculture, Institute of Animal Science, Agricultural Research Organization - Volcani InstituteEarlham Institute, Norwich Research ParkThe Roslin Institute, The University of EdinburghWorldFishEarlham Institute, Norwich Research ParkAbstract 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.https://doi.org/10.1186/s12864-022-09065-8Reference genomeTilapiaIntrogressionAquaculture |
| spellingShingle | G. J. Etherington W. Nash A. Ciezarek T. K. Mehta A. Barria C. Peñaloza M. G. Q. Khan A. Durrant N. Forrester F. Fraser N. Irish G. G. Kaithakottil J. Lipscombe T. Trong C. Watkins D. Swarbreck E. Angiolini A. Cnaani K. Gharbi R. D. Houston J. A. H. Benzie W. Haerty Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus BMC Genomics Reference genome Tilapia Introgression Aquaculture |
| 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 | Reference genome Tilapia Introgression Aquaculture |
| url | https://doi.org/10.1186/s12864-022-09065-8 |
| work_keys_str_mv | AT gjetherington chromosomelevelgenomesequenceofthegeneticallyimprovedfarmedtilapiagiftoreochromisniloticushighlightsregionsofintrogressionwithomossambicus AT wnash chromosomelevelgenomesequenceofthegeneticallyimprovedfarmedtilapiagiftoreochromisniloticushighlightsregionsofintrogressionwithomossambicus AT aciezarek chromosomelevelgenomesequenceofthegeneticallyimprovedfarmedtilapiagiftoreochromisniloticushighlightsregionsofintrogressionwithomossambicus AT tkmehta chromosomelevelgenomesequenceofthegeneticallyimprovedfarmedtilapiagiftoreochromisniloticushighlightsregionsofintrogressionwithomossambicus AT abarria chromosomelevelgenomesequenceofthegeneticallyimprovedfarmedtilapiagiftoreochromisniloticushighlightsregionsofintrogressionwithomossambicus AT cpenaloza chromosomelevelgenomesequenceofthegeneticallyimprovedfarmedtilapiagiftoreochromisniloticushighlightsregionsofintrogressionwithomossambicus AT mgqkhan chromosomelevelgenomesequenceofthegeneticallyimprovedfarmedtilapiagiftoreochromisniloticushighlightsregionsofintrogressionwithomossambicus AT adurrant chromosomelevelgenomesequenceofthegeneticallyimprovedfarmedtilapiagiftoreochromisniloticushighlightsregionsofintrogressionwithomossambicus AT nforrester chromosomelevelgenomesequenceofthegeneticallyimprovedfarmedtilapiagiftoreochromisniloticushighlightsregionsofintrogressionwithomossambicus AT ffraser chromosomelevelgenomesequenceofthegeneticallyimprovedfarmedtilapiagiftoreochromisniloticushighlightsregionsofintrogressionwithomossambicus AT nirish chromosomelevelgenomesequenceofthegeneticallyimprovedfarmedtilapiagiftoreochromisniloticushighlightsregionsofintrogressionwithomossambicus AT ggkaithakottil chromosomelevelgenomesequenceofthegeneticallyimprovedfarmedtilapiagiftoreochromisniloticushighlightsregionsofintrogressionwithomossambicus AT jlipscombe chromosomelevelgenomesequenceofthegeneticallyimprovedfarmedtilapiagiftoreochromisniloticushighlightsregionsofintrogressionwithomossambicus AT ttrong chromosomelevelgenomesequenceofthegeneticallyimprovedfarmedtilapiagiftoreochromisniloticushighlightsregionsofintrogressionwithomossambicus AT cwatkins chromosomelevelgenomesequenceofthegeneticallyimprovedfarmedtilapiagiftoreochromisniloticushighlightsregionsofintrogressionwithomossambicus AT dswarbreck chromosomelevelgenomesequenceofthegeneticallyimprovedfarmedtilapiagiftoreochromisniloticushighlightsregionsofintrogressionwithomossambicus AT eangiolini chromosomelevelgenomesequenceofthegeneticallyimprovedfarmedtilapiagiftoreochromisniloticushighlightsregionsofintrogressionwithomossambicus AT acnaani chromosomelevelgenomesequenceofthegeneticallyimprovedfarmedtilapiagiftoreochromisniloticushighlightsregionsofintrogressionwithomossambicus AT kgharbi chromosomelevelgenomesequenceofthegeneticallyimprovedfarmedtilapiagiftoreochromisniloticushighlightsregionsofintrogressionwithomossambicus AT rdhouston chromosomelevelgenomesequenceofthegeneticallyimprovedfarmedtilapiagiftoreochromisniloticushighlightsregionsofintrogressionwithomossambicus AT jahbenzie chromosomelevelgenomesequenceofthegeneticallyimprovedfarmedtilapiagiftoreochromisniloticushighlightsregionsofintrogressionwithomossambicus AT whaerty chromosomelevelgenomesequenceofthegeneticallyimprovedfarmedtilapiagiftoreochromisniloticushighlightsregionsofintrogressionwithomossambicus |