Etherington Graham, Ciezarek Adam, Mehta Tarang, Barker Tom, Durrant Alex, Fraser Fiona, Henderson Suzanne, Irish Naomi, Kaithakottil Gemy, Knitlhoffer Vanda, Ali Shimaa, Trong Trinh, Watkins Chris, Swarbreck David, Gharbi Karim, Benzie John, Haerty Wilfried
Earlham Institute, Norwich Research Park, Norwich, UK.
Department of Biochemistry, Cell and Systems Biology, University of Liverpool, Liverpool, UK.
Sci Rep. 2025 May 8;15(1):16057. doi: 10.1038/s41598-025-01300-y.
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.
尼罗罗非鱼（Oreochromis niloticus）作为一种水产养殖品种取得成功，部分原因是通过持续的选择性育种培育出了高性能品系。这些优良品系源自不同来源的育种群体，并与其他罗非鱼物种进行了杂交。由于每个品系都有复杂而独特的进化历史，野生种群现有的参考基因组不适合在水产养殖计划中对生长或环境适应能力等有益性状进行基因组选择。在此，我们结合PacBio HiFi和Illumina Omni-C测序技术，生成了世界鱼类遗传改良阿巴萨尼罗罗非鱼（GIANT）优良品系的高质量基因组组装和注释。由于用于基因组组装的是雄性阿巴萨尼罗罗非鱼，我们重建了X和Y单倍型，在LG23上鉴定出了amhY和amhΔy，这表明阿巴萨可能与吉富品系具有相同的性别决定系统，因此与现有的参考基因组不同，后者的性别决定位点位于LG1上。
