Abstract Amphioxus, as the best living proxy to the chordate ancestor, is considered an irreplaceable model organism for evolutionary studies of chordates and deuterostomes. In this study, a high-quality genome of the Beihai amphioxus, Branchiostoma belcheri beihai, was de novo assembled and annotated. Within four amphioxus genomes, a wide range of gene novelties were identified, revealing new genes that share unexpectedly high similarities with those from non-metazoan species. These gene innovation events have played roles in a range of amphioxus adaptations, including innate immunity responses, adaptation to anaerobic environments, and regulation of calcium balance. The gene novelties related to innate immunity, such as a group of lipoxygenases and a DEAD-box helicase, boosted amphioxus immune responses. The novel genes for alcohol dehydrogenase and ferredoxin could aid in the anaerobic tolerance of amphioxus. A proximally arrayed cluster of EF-hand calcium-binding protein genes were identified to resemble those of bacteria. The copy number of this gene cluster was linearly correlated to the sea salinity of the collection region, suggesting that it may enhance their survival at different calcium concentrations. Collectively, this comprehensive study on gene novelties of amphioxus reveals insights into the early genome evolution of chordates and deuterostomes and provides valuable resources for future research.

Gene Novelties in Amphioxus Illuminate the Early Evolution of Deuterostomes