Pangenomics developments for UK aquaculture species

For the last 30 years the outputs of wild capture fisheries have plateaued mainly due to the impact of over exploitation of the existing stocks. 

The assessment of the genetic diversity and population structure within a species are keys in establishing the sustainability of this species. Genomics offers the unprecedented potential to accurately delineate fisheries stocks. 

This enables better fisheries management, by identifying biologically relevant management units. To date, fisheries genomics studies have relied on at best a single reference genome, which represents the genetic content of only one individual thereby limiting investigations to genetic variation identified within only homologous regions. 

Here though a highly collaborative project between Cefas (Dr David Murray, Dr Adam Ciezarek) and the Earlham Institute (Dr Wilfried Haerty) we propose to apply a pangenomic approach to quantify the genetic diversity of the UK populations of two major aquaculture species: the pollack, and herring.

Through the completion of this project the candidate will gain highly transferable skills (bioinformatics, genome assembly, population genomics).

Application Information:

• Apply by 23.59 on Wednesday 26 March 2025
• Visit the UEA website for further information on eligibility, funding and how to apply: https://www.uea.ac.uk/apply/postgraduate/research
• You can also visit: https://www.earlham.ac.uk/application-guidance

Related Reading:

• Ciezarek AG, Mehta TK, Man A, Ford AGP, Kavembe GD, Kasozi N, Ngatunga BP, Shechonge AH, Tamatamah R, Nyingi DW, Cnaani A, Ndiwa TC, Di Palma F, Turner GF, Genner MJ, Haerty W. Ancient and Recent Hybridization in the Oreochromis Cichlid Fishes. Mol Biol Evol. 2024 Jul 3;41(7):msae116. doi: 10.1093/molbev/msae116. PMID: 38865496; PMCID: PMC11221657.
• Etherington GJ, Nash W, Ciezarek A, Mehta TK, Barria A, Peñaloza C, Khan MGQ, Durrant A, Forrester N, Fraser F, Irish N, Kaithakottil GG, Lipscombe J, Trong T, Watkins C, Swarbreck D, Angiolini E, Cnaani A, Gharbi K, Houston RD, Benzie JAH, Haerty W. Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus. BMC Genomics. 2022 Dec 15;23(1):832. doi: 10.1186/s12864-022-09065-8. PMID: 36522771; PMCID: PMC9756657.