Comparative genomics and evolutionary analyses of the O-methyltransferase gene family in Populus Abdelali Barakat a, ⁎ ,1 , Alex Choi a , Norzawani Buang M. Yassin a , Joseph S. Park a , Zichao Sun a,2 , John E. Carlson a,b a The School of Forest Resources and The Huck Institutes of the Life Sciences, The Pennsylvania State University, 326 Forest Resources Building, University Park, PA 16802, USA b The Department of Bioenergy Science and Technology (WCU), Chonnam National University, 333 Yongbongro, Buk-Gu, Gwangju 500-757, Republic of Korea abstract article info Article history: Accepted 13 February 2011 Available online 19 February 2011 Received by A.J. van Wijnen Keywords: Lignin Evolution Expression Duplication Stress 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. © 2011 Elsevier B.V. All rights reserved. 1. Introduction S-adenosyl-L-methionine (SAM) dependent O-methyltransferases (OMTs) are proteins that catalyze the methylation of small molecules such as flavonoids, alkaloids, phytoalexins, lignin precursors, etc. (Lam et al., 2007). Plant methyltransferases were classified into three main classes based on their substrates: O-methyltransferases (OMTs), N-methyltransferases (NMTs), and C-methyltransferases (CMTs) (Roje, 2006). OMTs were further classified into five classes based on substrate specificity (Roje, 2006). Class A includes caffeoyl coenzyme A 3-O-methyltransferase (CCoAOMT) and caffeic acid 3-O-methyl- transferase (COMT) proteins, which act on the hydroxyl groups of phenylpropanoids. Genes from class B, C, and D are involved in the methylation of hydroxyl groups within flavonoids, alkaloids, and myo- inositol O-methyltransferase, respectively (Rammesmayer et al., 1995; Roje, 2006). A fifth class of OMT proteins methylates the carboxyl group of various acids (Roje, 2006). An early study (Joshi and Chiang, 1998) showed that OMT genes were distributed into two distinct groups (PL-OMT I and PL-OMT II) based on sequence similarity and protein signature motifs. Genes from the PL-OMT I group represented mainly by CCoAOMT sequences are involved in lignin biosynthesis and use only a pair of substrates (caffeoyl CoA and 5-hydroxyferuloyl CoA). PL-OMT II group was represented by COMT and other OMT proteins acting on a variety of substrates, such as caffeic acid (CA), 5-hydroxyferulic acid (5HFA), caffeoyl CoA ester, 5-hydroxyferuloylester, myo-inositol, chalcones and scoulerine (Joshi and Chiang, 1998). Conserved protein motifs involved in the binding of S-adenosyl methionine, which is a common methyl donor of a large variety of methyltransferases in plants, specific to SAM-OMT from PL-OMT I and PL-OMT II were reported (Joshi and Chiang, 1998). Gene 479 (2011) 37–46 Abbreviations: OMT, O-methyltransferase; COMT, caffeic acid O-methyltransferase; nt, nucleotide; aa, amino acid; RT-PCR, reverse transcriptase polymerase chain reaction; CCoAOMT, caffeoyl CoA-methyltransferase; FAH, ferulic acid hydroxylase; SAM, S- adenosyl-L-methionine; AEOMT, hydroxycinnamic acids/hydroxycinnamoyl CoA esters O-methyltransferase; in, intron; ex, exon. ⁎ Corresponding author at: Department of Genetics and Biochemistry, Clemson University, 100 Jordan Hall, Clemson, SC 29634, USA. Tel.: +1 864 656 3060; fax: +1 864 656 6879. E-mail address: abaraka@clemson.edu (A. Barakat). 1 Current address: Department of Genetics and Biochemistry, Clemson University, 100 Jordan Hall, Clemson, SC 29634, USA. 2 Current address: University of Michigan School of Public Health, 1415 Washington Heights, 1700 SPH I, Ann Arbor, MI 48109-2029, USA. 0378-1119/$ – see front matter © 2011 Elsevier B.V. All rights reserved. doi:10.1016/j.gene.2011.02.008 Contents lists available at ScienceDirect Gene journal homepage: www.elsevier.com/locate/gene