S-adenosyl-l-methionine (SAM) dependent O-methyltransferases (OMTs) proteins are involved in the methylation of various secondary metabolites. The OMT genes have been studied in various plants, but these studies focused either on a single or a small set of genes. Moreover, no comprehensive study was published yet on the OMT gene family in a tree species. To investigate the evolutionary history of this gene family and the functional diversification of its members, phylogenetic and several comparative genomics analyses were performed. Phylogeny across land plant lineages showed that OMT genes were distributed in two main classes deeply rooted in the phylogeny of land plants, suggesting that they have evolved by a gene duplication that had happen in the ancestor of land plants. COMT and COMT-like genes were clustering with few flavonoid and multifunctional OMT genes in class II. Class I included flavonoid, simple phenol, and multifunctional OMT genes. All 26 Populus OMT genes were located in segmental duplication blocks and two third of them were tandem duplicated, indicating the role of duplication processes in the expansion of this gene family. Expression profiling of OMT genes in Populus showed that only PoptrOMT25 was differentially expressed in xylem. The other genes were differentially expressed in leaves, bark, or both. Some OMT genes showed differential expression patterns under various biotic and abiotic stresses. The divergence of protein sequences, the phylogenetic distribution, and the expression of COMT and COMT-like genes suggest that they have evolved different functions or tissue specificities following duplications.
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