Barvkar et al. BMC Genomics 2012, 13:175 http://www.biomedcentral.com/1471-2164/13/175 modification that alters their activity, sub-cellular loca- tion and modulates their chemical properties, such as solubility and stability, which are important for their in planta functions [5]. The glycosylation process is catalyzed by glycosyltransfer- ase enzymes (GTs), which are highly divergent, polyphyletic and belong to a multigene family found in all living organisms [6]. GTs from diverse species have been classified into 92 families based on the amino acid sequence similarities, catalytic mechanisms and the presence of conserved sequence motifs (http://www.cazy.org/ GlycosylTransferases.html). Among these, the glycosyl- transferase family 1 is the largest family, the enzymes of which generally catalyze transfer of the glycosyl group from nucleoside diphosphate-activated sugars (e.g., UDP-sugars) to a diverse array of substrates, including hormones, secondary metabolites and xenobio- tics such as pesticides and herbicides [5,7]. The plant UGT enzymes are characterized by a unique, well-conserved sequence of 44 amino acid residues designated as the plant secondary product glycosyltransferases (PSPG) box [8] and a catalytic mechanism that inverts the anomeric configur- ation of a transferred sugar [9]. The GT family 1 has been extensively studied in various plants species, as well as in humans. In mammals, UGTs coordinate the activity of signal molecules such as steroid hormones and detoxify xenobiotic compounds taken up from the environment [10]. Polymorphisms among these UGTs have been shown to be associated with increased susceptibility to certain diseases in humans [11]. Studies in model plants have shown that the plant genomes contain a great diversity of gene sequences predicted to be involved in glycosylation [12,13]. The occurrence of a wide range of glycosylated products in flax [3] suggests the presence of a large number of UGTs. The availability of the flax genome sequence (http://linum.ca), tissue specific ESTs (http://www. ncbi.nlm.nih.gov/nuccore?term=Linum%20usitatissimum) and microarray expression dataset [14] (http://www.ncbi. nlm.nih.gov/projects/geo/) of flax provide an opportunity to analyze the diversity of expressed glycosyltransferase family genes in this economically important oilseed crop. In this study, we identified 137 UGT genes from flax, which were clustered into 14 phylogenetically distinct groups. Their expression patterns were analyzed using 15 tissue specific EST libraries available at the NCBI as well as the publicly available microarray expression data, which indicated their differential expression in various flax tissues. This digital expression analysis was further supported by RT-qPCR for ten selected genes. Seven flax diverged UGTs were identified from the families 75, 79 and 94, which indicated diversification of flax UGTs as compared to those of four other sequenced dicots, viz., Ricinus communis, Populus trichocarpa, Vitis vinifera and Arabidopsis thaliana. Page 2 of 13 Results Identification of flax UGT genes BlastP search against the 47,912 flax gene models (http://linum.ca) using the conserved PSPG box sequence resulted in the identification of 179 scaffolds. Family 1 UGTs usually utilize low molecular weight compounds as acceptor substrates and UDP-sugars as donors [12] and commonly possess a carboxy terminal consensus sequence (PSPG box) believed to be involved in binding to the UDP moiety of the sugar nucleotide donor [9,15]. Taking these characteristics into account, 137 sequences (GenBank accession numbers JN088282-JN088418) having lengths of 375–530 amino acids and 0–2 introns were selected and subjected to phylogenetic and digital expression analysis. In order to confirm the open reading frame (ORF) sequence of these genes, 11 genes expressed in seed tissue were randomly selected, isolated using PCR, cloned and sequenced, which revealed that they were 100% identical to the putative UGT gene sequences identified. Phylogenetic analysis All the identified putative UGT genes were classified as per the recommendations of the UGT Nomenclature Committee [6] (Additional file 1). As expected, the PSPG signature motif was present in all the UGT sequences and the overall sequence similarity among them varied substantially from 36% to 98% (Additional file 2). A total of 409 amino acid positions (60.41% of the sequences) were aligned for all the genes analyzed and used to con- struct a phylogenetic tree. Fourteen major groups (A-N) were defined by both the neighbour-joining (NJ) and parsimony methods with high bootstrap supports (>85) (Figure 1). The tree topology and grouping of the UGTs were similar as described for the Arabidopsis UGT genes [16], e.g. group L consists of the UGTs belonging to the families 74, 75 and 84. However, in four groups, A, C, G and I, sequences from additional UGT families were observed viz. LuUGT94, LuUGT97, LuUGT709 and LuUGT712, respectively. The number of genes (1–22) as well as the sequence diversity varied considerably within each group (Additional file 2). Detection of orthologs and duplicated genes The orthologs of flax UGTs identified in the four selected dicots are listed in the Additional file 3. Of the 137 sequences, orthologs were identified for 130 UGTs from at least one of the four dicots. However, for 72 sequences, orthologs were identified from all the four species. The maximum number of orthologs (125) was identified in case of Vitis vinifera, while the lowest of 80 orthologs were detected in case of Arabidopsis thaliana. Seven flax diverged UGTs were identified (LuUGT94G1, LuUGT94G2, LuUGT94G3, LuUGT94G4, LuUGT94H1,