Lineage-Specific Diversification of Nucleoporin Nup98 Genes in Ciliates and Its Evolutionary Implications for the Nuclear Dualism

Nup98 is a key component of the nuclear pore complex that plays essential roles in nucleocytoplasmic transport and gene regulation. To investigate the evolutionary diversification of Nup98 in ciliates, homologous sequences were collected from genomic and transcriptomic databases representing major ciliate lineages. Most species possessed multiple Nup98 paralogs, indicating that gene duplication events have occurred repeatedly during ciliate evolution. Phylogenetic analyses based on the conserved Nucleoporin2 domain revealed that Nup98 proteins from each ciliate class tend to form distinct monophyletic groups, suggesting lineage-specific diversification patterns. These results are consistent with a scenario in which early ciliates possessed a limited number of Nup98 genes, followed by independent duplication and diversification events in multiple lineages. However, alternative evolutionary scenarios remain possible. Differences in repeat motif composition were observed among paralogs across lineages, although these patterns were not conserved across all ciliates. While such variation may suggest potential functional diversification, phylogenetic evidence alone does not demonstrate functional differences among paralogs. Overall, the present diversity of Nup98 genes in ciliates is best interpreted as the result of lineage-specific evolutionary processes. These findings provide a framework for understanding Nup98 evolution and generate testable hypotheses regarding its potential roles in the diversification of nuclear dualism.