Chromosomal-level genome assembly of 8 Caenorhabditis nigoni intraspecies genome
A major topic in evolutionary biology is how sequence divergence shapes the establishment of reproductive barriers. Comparative genomic studies typically reveal systematic insights into intra- and interspecific divergence, thereby shedding light on speciation mechanisms. Despite the tremendous implications of Caenorhabditis briggsae and C. nigoni as model nematodes for speciation research, the genomic foundation of their sequence divergence remains poorly understood. Here, we performed a pan-genome-level comparative analysis between populations of these two species. We discovered consistently larger genome sizes and higher gene numbers in C. nigoni strains relative to C. briggsae strains, aligning with their asymmetrical gene flow. The augmented genome size of C. nigoni is primarily attributed to disproportionately larger unaligned regions, whereas the increased gene number mainly stems from the proliferation of C. nigoni-specific gene families. Further analysis revealed that both features are largely driven by the expansion of protein-degradation-related genes, particularly F- box genes, which likely reflect species-specific immune responses. Finally, through detailed characterization of the fbxn gene family, an F-box gene family containing the first identified nematode interspecific speciation gene, we demonstrated how extensive polymorphism within such gene families contributes to reproductive barriers. Our findings illuminate the genomic underpinnings of divergence between the two nematode species and underscore the pivotal role of protein degradation and immune responses in speciation.