A Comparative Genomic Survey Provides Novel Insights into Molecular Evolution of l-Aromatic Amino Acid Decarboxylase in Vertebrates.

Melatonin is a pleiotropic molecule with various important physiological roles in vertebrates. l-aromatic amino acid decarboxylase (AAAD) is the second enzyme for melatonin synthesis. By far, a clear-cut gene function of AAAD in the biosynthesis of melatonin has been unclear in vertebrates. Here, we provide novel insights into the evolution of AAAD based on 77 vertebrate genomes. According to our genome-wide alignments, we extracted a total of 151 nucleotide sequences. A phylogenetic tree was constructed on the basis of these sequences and corresponding protein alignments, indicating that tetrapods and diploid bony fish genomes contained one gene and a new -like gene, which formed a novel AAAD family. However, in tetraploid teleosts, there were two copies of the gene due to whole genome duplication. A subsequent synteny analysis investigated 81 sequences and revealed their collinearity and systematic evolution. Interestingly, we discovered that platypus (, Atlantic cod (), Mexican tetra (), and a cavefish () have long evolutionary branches in the phylogenetic topology. We also performed pseudogene identification and selection pressure analysis; however, the results revealed a deletion of 37 amino acids in Atlantic cod and premature stop codons in the cave-restricted and , suggesting weakening or disappearing rhythms in these cavefishes. Selective pressure analysis of between platypus and other tetrapods showed that rates of nonsynonymous () and synonymous () substitutions were higher when comparing the platypus to other representative tetrapods, indicating that, in this semiaquatic mammal, the gene experienced selection during the process of evolution. In summary, our current work provides novel insights into genes in vertebrates from a genome-wide view.