# Reconstruction of the X and Y haplotypes in the genetically improved Abbassa nile tilapia genome assembly

## TL;DR

This paper presents a high-quality genome assembly of a genetically improved Nile tilapia strain and identifies its sex determination system.

## Contribution

The study provides a new genome assembly for the Abbassa Nile tilapia and reconstructs X and Y haplotypes, revealing its shared sex determination system with another strain.

## Key findings

- A high-quality genome assembly was generated for the Abbassa Nile tilapia using PacBio HiFi and Omni-C Illumina sequencing.
- Both X and Y haplotypes were reconstructed, identifying amhY and amhΔy on LG23.
- The Abbassa strain shares the same sex determination system as GIFT, differing from the existing reference genome.

## Abstract

The success of the Nile tilapia (Oreochromis niloticus) as an aquaculture species is partly the result of continuous selective breeding leading to high performing strains. These elite strains have been derived from breeding populations of diverse origins and crosses with other Oreochromis species. Owing to the complex and unique evolutionary histories of each strain, existing reference genomes of wild populations are unsuitable to implement genomic selection for beneficial traits such as growth or environmental resilience in aquaculture programmes. Here we generated a high-quality genome assembly and annotation of the WorldFish Genetically Improved Abbassa Nile tilapia (GIANT) elite strain using a combination of PacBio HiFi, and Omni-C Illumina sequencing. As a male Abbassa Nile tilapia was used for the generation of the genome assembly, we reconstructed both X and Y haplotypes, identifying both amhY and amhΔy on LG23 indicating that Abbassa likely shares the same sex determination system as GIFT, and thereby differs from the existing reference genome, whose sex determination loci are located on LG1.

The online version contains supplementary material available at 10.1038/s41598-025-01300-y.