Chromosome-level genome of Coptodon zillii reveals adaptive evolution and invasion mechanisms

Understanding the adaptive mechanisms of invasive fish is crucial for studying their evolution and designing effective control measures. The redbelly tilapia ( Coptodon zillii ) is a widespread and invasive tilapiine species with a strong ability to adapt to new environments where it alters ecosystem structure and function. To investigate the mechanism of its rapid invasion, we generated a chromosome-level genome assembly using Illumina, PacBio, and Hi-C technologies, followed by population resequencing (79 individuals across three native Ethiopian and five invasive Chinese populations). The final genome assembly spanned 980.04 Mb, featuring a 34.72 Mb contig N50. Contigs were mapped to 22 pseudochromosomes (scaffold N50: 40.09 Mb), predicting 29,033 protein-coding genes with 96.87% functional annotation. We identified three significantly expanded gene families linked to adaptation and invasiveness, including olfactory receptors, C-type lectin receptors, and B7 co-stimulatory molecules. Two Immune response-related genes under positive selection may have facilitated rapid environmental adaptation in redbelly tilapia. Population genomic analyses revealed three ancestral sources for China's invasive populations. Selective sweep analysis showed that candidate genes associated with local adaptation were functionally correlated with olfactory signal transduction, immune response, antioxidant defence, and stress response. In conclusion, this high-quality reference genome serves as a valuable resource for studying invasive tilapia genomics, aiding investigations into redbelly tilapia's successful invasion mechanisms. We have also produced genetic resources for developing new management strategies for invasive fishes.