Amphioxus as a model for investigating evolution of the vertebrate immune system

•The digestive system is the major defense line of cephalochordate amphioxus.•Amphioxus has lymphocyte-likes cells, macrophage-like cells and monocyte-like cells.•Amphioxus has some basic components of vertebrate adaptive immunity (VAI).•Amphioxus has an extraordinarily complex innate immunity, created by huge expansions of many innate gene families.•Amphioxus has unique features to become an important model for understanding the phylogeny of immunity. As the most basal chordate, the cephalochordate amphioxus has unique features that make it a valuable model for understanding the phylogeny of immunity. Vertebrate adaptive immunity (VAI) mediated by lymphocytes bearing variable receptors has been well-studied in mammals but not observed in invertebrates. However, the identification of lymphocyte-like cells in the gill along with genes related with lymphoid proliferation and differentiation indicates the presence of some basic components of VAI in amphioxus. Without VAI, amphioxus utilizes about 10% of its gene repertoires, and an ongoing domain reshuffling mechanism among these genes, for innate immunity, suggesting extraordinary innate complexity and diversity not observed in other species. Innate diversity may not be comparable to the somatic diversity of the VAI, but there is no doubt of the success of this immune system, since amphioxus has existed for over 500 million years. Studies of amphioxus immunity may provide information on the reduction of innate immune complexity and the conflict between microbiota and host shaped the evolution of adaptive immune systems (AIS) during chordate evolution.