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.
METHODS: The study was focused on assessing the impact of tilapia culture at sites nearer to the AIZ vs more distant sites, the former with a greater likelihood of receiving escapees. Two major sites were chosen; within 5 km (near-cage) and within 5-15 km (far-cage) radii from the AIZ. Fish sampling was conducted using multiple mesh sizes of gill nets (3.7, 5.1, 6.5, 7.6, and 10.2 cm) deployed at the littoral zone of the sampling points. Species diversity, abundance, dietary habits, and habitat preference were investigated.
RESULTS: The CPUE (individual/hour) of native fish species at the far-cage site of the AIZ Reservoir was found to be significantly higher (p < 0.05) than that at the near-cage site. Principal component analysis (PCA) based on diet and habitat preferences showed that the tilapia, O. niloticus had almost overlapping diet resources and habitat with native fish species.
CONCLUSION: We conclude that there is a correlation between the reduced catches of native species (based on CPUE) and the high presence of tilapia. Thus, appropriate actions must be implemented for strategic and effective planning in terms of native fish conservation.