LAUSR

Significance Carotenoids are isoprenoids lipids found in many prokaryotes and eukaryotes with important physiological implications, including antioxidative functions and modulating membrane properties. Here, we unveil a biosynthetic pathway of C30 carotenoids that uses squalene as a precursor, simultaneously showing that this route is widespread in bacteria. This new pathway expands the functional repertoire of the squalene which has been exclusively associated to the synthesis of polycyclic triterpenes, such as sterols. Reconstructing the carotenoid amino oxidases evolution, we infer two main origins of these carotenoid pathways, showing that these routes have been spread by lateral gene transfer between prokaryotes and readapted once acquired. Together, we provide a comprehensive understanding for the biosynthesis and evolution of carotenoid pathways in an extensive diversity of prokaryotes.