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The complete sequencing of genomes and the development of in silico methods for identification of genes encoding selenocysteine (Sec)-containing proteins have greatly contributed to shape our view on the evolution of selenium utilization in nature. Current evidence is consistent with the idea that Sec decoding is a late addition to the genetic code and it evolved once, before the separation of archaeal, bacterial and eukaryal domains. Many organisms have lost the Sec decoding trait, but recent evidence has shown that the loss is not irreversible. The distribution of organisms that use UGA as a Sec codon suggests that Sec decoding evolved as a result of speciation, differential gene loss and horizontal gene transfer. Selenium is also used in the synthesis 2-selenouridine, a modified base of unknown function located in the wobble position of certain tRNAs. It has been recently demonstrated that selenouridine and Sec-decoding traits can evolve independently of each other, but both require selenophosphate synthetase. This ATP-dependent enzyme emerged as a key feature of selenium utilization that allows separation of selenium from the pathways of sulfur utilization and non-specific use of selenium. Some animals, including mammals, evolved two selenophosphate synthetases, highlighting an unknown complexity of selenium utilization in nature.