Barvkar et al. BMC Genomics 2012, 13:175 http://www.biomedcentral.com/1471-2164/13/175 R E S E A R C H A R T I C L E Open Access Phylogenomic analysis of UDP glycosyltransferase 1 multigene family in Linum usitatissimum identified genes with varied expression patterns Vitthal T Barvkar, Varsha C Pardeshi, Sandip M Kale, Narendra Y Kadoo and Vidya S Gupta* Abstract Background: The glycosylation process, catalyzed by ubiquitous glycosyltransferase (GT) family enzymes, is a prevalent modification of plant secondary metabolites that regulates various functions such as hormone homeostasis, detoxification of xenobiotics and biosynthesis and storage of secondary metabolites. Flax (Linum usitatissimum L.) is a commercially grown oilseed crop, important because of its essential fatty acids and health promoting lignans. Identification and characterization of UDP glycosyltransferase (UGT) genes from flax could provide valuable basic information about this important gene family and help to explain the seed specific glycosylated metabolite accumulation and other processes in plants. Plant genome sequencing projects are useful to discover complexity within this gene family and also pave way for the development of functional genomics approaches. Results: Taking advantage of the newly assembled draft genome sequence of flax, we identified 137 UDP glycosyltransferase (UGT) genes from flax using a conserved signature motif. Phylogenetic analysis of these protein sequences clustered them into 14 major groups (A-N). Expression patterns of these genes were investigated using publicly available expressed sequence tag (EST), microarray data and reverse transcription quantitative real time PCR (RT-qPCR). Seventy-three per cent of these genes (100 out of 137) showed expression evidence in 15 tissues examined and indicated varied expression profiles. The RT-qPCR results of 10 selected genes were also coherent with the digital expression analysis. Interestingly, five duplicated UGT genes were identified, which showed differential expression in various tissues. Of the seven intron loss/gain positions detected, two intron positions were conserved among most of the UGTs, although a clear relationship about the evolution of these genes could not be established. Comparison of the flax UGTs with orthologs from four other sequenced dicot genomes indicated that seven UGTs were flax diverged. Conclusions: Flax has a large number of UGT genes including few flax diverged ones. Phylogenetic analysis and expression profiles of these genes identified tissue and condition specific repertoire of UGT genes from this crop. This study would facilitate precise selection of candidate genes and their further characterization of substrate specificities and in planta functions. Background Flax or linseed (Linum usitatissimum L.) is one of the earliest domesticated crops. It is a self-pollinating diploid species cultivated as a source of fibre, oil and medicinal compounds. Historically it has been used as a model for developmental studies and has a different evolutionary history than other model plants like Arabidopsis [1]. Among plant foods, flaxseed has the highest contents of the essential omega-3 fatty acid, alpha-linolenic acid * Correspondence: vs.gupta@ncl.res.in Plant Molecular Biology Group, Biochemical Sciences Division, National Chemical Laboratory, Pune, 411008, India (ALA) [2] and bioactive phenolic compounds such as lignans, predominantly secoisolariciresinol diglucoside (SDG) [3], phenolic acids and flavonoids [4]. ALA dampens inflammatory reactions, thereby reducing a risk of heart attack or stroke; while lignans are strong antioxidants inhibiting breast and prostate cancers. Given the economic and health benefits of these bioactive compounds, it would be useful to comprehensively analyze the genes involved in their biosynthesis. In plants, glycosylation represents the last step in the biosynthesis of numerous natural compounds like terpenes, phenylpropanoids, cyanogenic glucosides and glucosinolates. It is an important © 2012 Barvkar et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.