The organelle paralogy hypothesis (OPH) aims to explain the evolution of organelles that did not originate from endosymbiosis. It predicts that lineage-specific pathways or organelles should emerge when identity-encoding membrane-trafficking components duplicate and co-evolve. In this study, we explore the presence of such lineage-specific membrane-trafficking machinery paralogs in Apicomplexa, a significant parasitic lineage. We identified 18 paralogs of known membrane-trafficking machinery, often associated with the presence of new endomembrane organelles in apicomplexans or their parent lineage, the Alveolata. Additionally, a focused analysis of the apicomplexan Arf-like small GTPases (e.g., ArlX3) revealed a specific post-Golgi trafficking pathway involved in delivering proteins to micronemes and rhoptries. Knockdown experiments demonstrated reduced invasion capacity, indicating the pathway's role in invasion. Overall, our findings reveal an unexpected post-Golgi trafficking pathway in apicomplexans and support the OPH mechanism in generating endomembrane pathways or organelles at various evolutionary stages across the alveolate lineage.
