Barvkar et al. BMC Genomics 2012, 13:175 http://www.biomedcentral.com/1471-2164/13/175 expression of LuUGT85Q1 in stem, root and mature seed (i.e. 48 DAF) suggest the putative function as cyanogenic glycosyltransferases [20]. LuUGT74S1 expressed highly in developmental seed stages and peaked at 12 DAF i.e. torpedo stage of embryo. Flax has a major lignan, secoi- solariciresinol diglucoside, which is a phenylpropanoid and accumulates in seed coat [21]. UGTs belonging to the gene family 74 glycosylate phenylpropanoid group of compounds. About 25 ESTs clones from torpedo stage seed coat library were mapped on LuUGT74S1 gene indi- cating its putative in planta function as secoisolariciresi- nol glycosyltransferase. Expression profiles of the 10 selected genes analyzed using RT-qPCR, matched well with the digital expression results. Discussion Glycosylation mediated by glycosyltransferase enzymes (GTs) is a critical step in metabolic pathways with diverse roles in cellular processes and homeostasis [22]. Recent studies involving functional characterization of plant GTs suggest their important roles in growth, development and interaction with the environment [9]. The activities of many GTs from a variety of plants and biological roles of their products have been known for a long time [23]. However, the methods for identification of UGTs based on biochemical and classical genetic approaches are slow and difficult [15]. Recent developments in plant genomics stimulated the use of strategies such as differential display methods and/or homology-based screening of cDNA libraries for identification and isolation of novel UGT genes [24-26], although the roles of many UGTs still remain uncertain. Availability of whole genome sequence of many plants enabled a thorough and detailed analysis of multigene families. For example, in Arabidopsis, genome-wide search using PSPG motif identified 120 putative UGT genes. Similarly, a whole genome survey of six plant species resulted in identification of 56 (Carica papaya) to 242 (Glycine max) UGTs [27]. The recently published draft genome sequence and the extensive tissue specific EST library collections of flax provided an opportunity to investigate the diversity in flax UGT multigene family in a greater detail. We identified 137 flax UGTs, which is more than that identified in Arabidopsis but less than that discovered in rice, grapevine and Medicago [27]. All the identified UGTs contain two major domains, a conserved C-terminal domain and a variable N-terminal domain, although the overall sequence diversity was high among the genes. Flax UGT family resembles the phylogenetic group structure of Arabidopsis UGTs A phylogenetic tree provides a framework to compare the properties of gene family members and to identify similarities and differences among them [28]. In the Page 8 of 13 present study, the flax genome revealed 22 UGT families including four new families (94, 97, 709 and 712), not reported in Arabidopsis. However, phylogenetic analysis of flax UGTs clustered them in 14 groups (A-N) as reported in Arabidopsis [7,12] and interestingly, the four new flax UGT families did not form any additional groups. Moreover, all the six sequences of the UGT94 family clustered with the Sesamum indicum UGT94D1 sequence (BAF99027 [29]), and UGT94B1 (AB190262 [30]) are the only UGT94 family sequence reported till now. A phylogenetic tree constructed by Bowles et al. [31] using 22 UGT sequences reported from other plant species along with the Arabidopsis UGT sequences, mostly resulted in 14 groups, while an additional group of cytokinin GTs was identified containing the Phaseolus vulgaris and Zea mays UGT sequences [31,32]. Based on the phylogenetic analysis of Arabidopsis UGTs, it has been shown that it might be possible to correlate, to a large extent, the regiospecificity of glycosylation to the phylogenetic groups [33]. The exception to this might be due to regioswitching events taking place during evolu- tion. In some cases, phylogenetically closely related UGTs show distinct regiospecific differences towards a common acceptor. For example, A. thaliana UGTs, AtUGT74F1 and AtUGT74F2, share ~82% amino acid sequence identity, and while AtUGT74F1 glucosylates the phenolic hydroxyl group of 2-hydroxy benzoic acid, AtUGT74F2 glucosylates both the carboxyl and hydroxyl groups of 2-hydroxy benzoic acid [34]. On the contrary, in some cases (e.g. UGT85B1), the genes have been shown to exhibit a broad specificity toward acceptors in vitro; however, a member of this group (UGT85Q1) in Sorghum bicolor specifically catalyzes the conversion of p-hydroxymandelonitrile into dhurrin in vivo [35]. This analysis, along with amino acid sequence similarity of UGT families within a group, might be useful for predicting substrates [31,36]. For example, Osmani et al. [37] reported that the group G members glycosylate terpenoids; while the members of groups D, E and L glycosylate flavaonoids, tepenoids and benzoates. However, a study of several Medicago truncatula UGTs highlighted the difficulties in assigning substrate specificity based on phylogeny. Biochemical and phylogenetic studies of MtUGT78G1 and MtUGT85H2 showed that substrate specificity could not be predicted by their clustering with biochemically characterized UGTs belonging to the same family [38]. Although, few genomes such as rice, poplar, grapevine and Medicago have been screened and annotated for GT genes, they have not been assigned to GT groups and families so far. Apart from the model plant Arabidopsis [12], this is the first attempt to classify GT genes into groups and families from a crop plant flax, as per the standardized system recommended by the UGT Nomenclature Committee [6]. Thus, the