Barvkar et al. BMC Genomics 2012, 13:175 http://www.biomedcentral.com/1471-2164/13/175 LuUGT75N3 and LuUGT79A4) and 22 gene duplication events with sequence similarity of ~90% were observed (Additional file 4). Analysis of intron gain/loss events Among the 137 sequences, 55 were intron less, while 72 and 10 had one and two introns each, respectively (Additional file 1). Total 92 introns were detected in the 137 UGTs, with an average of 0.67 intron per gene. Seven independent intron insertion events were observed when the intron positions were compared with the sequence relationship predicted by the phylogenetic analysis (Figure 2). An intron was considered conserved if its position in a particular sequence was within 40–45 amino acids of its mean recorded position across the sequences (for complete sequence alignment see Additional file 5: Figure S1). Two conserved introns (intron 3 and intron 4; Additional file 1) were identified, of which intron 3 was observed in 44 UGTs belonging to the A, C and F-J phylogenetic groups, while intron 4 was observed in 27 UGTs belonging to the D, E, K and L phylogenetic groups. LuUGT79A4 from group A and LuUGT709E3 from group G both had the conserved introns. Alternatively, group M showed absence of both the conserved introns, while LuUGT92G2 from group M showed gain of intron 5. Within the members of groups F-J and N, intron 3 was predominant, except in LuUGT85Q2 and LuUGT87J2. In comparison, the members of groups K and L had intron 4, while only one member of L group (LuUGT74S1) showed the presence of intron 3. All other introns were either found only within a single restricted group of closely related sequences or in only a single gene. Group B members were intron less. Many sequences showed loss of the conserved introns and gain of other introns. For example, within group A, three members from family 79 and one member from family 91 (LuUGT91J3) showed loss of conserved introns 3 and 4, and gain of introns 5 and 6, respectively. Similarly, within group D, four members of family 73 lost conserved intron 4 and few members gained introns 2, 5 and 7. Likewise, in group E, all the members of the family 71 showed loss of conserved intron 4 while gain of introns 1, 7 and 8 in few members. Most of the conserved introns were either in phase 1 (49 genes) or phase 0 (15 genes) (Additional file 1). The intron sizes of flax UGTs ranged from 65 bp to 2258 bp with an average of 406 bp for both the introns. About 28% of the flax UGT introns were in the size range of 65–99 bp (Additional file 6: Figure S2). In Arabidopsis, 37 out of 88 UGT genes contained introns while, three genes had two introns. By comparing the intron positions with sequence relationships predicted by phylogenetic analysis, a minimum of nine independent intron insertion events appear to have happened in the Page 4 of 13 course of UGT evolution in Arabidopsis. Intron 2 was found to be widespread and oldest intron and was present in all of the 23 UGT sequences in groups F–K in Arabidopsis [12]. Similarly in flax, the introns 3 and 4 have been found in most members of the groups F-J and K respectively and could be considered as the oldest introns. Expression analysis of flax UGT genes using EST data Expression of the identified UGT genes was analyzed using the available EST and microarray data of flax. Of the 137 genes, 100 genes showed expression evidence based on either or both the datasets. Among these, 85 genes (62.04%) were expressed based on the EST data; while the microarray data indicated expression evidence for 60 genes (43.79%) (Additional file 7). Similarly for 45 genes, the expression evidence was present in both the datasets. Further, the ESTs from various flax tissues were mapped onto the 137 flax UGT gene models to estimate their gene expression levels. This analysis identified that a total of 325 ESTs mapped to 85 flax UGT sequences with an average of 3.82 ESTs per gene. The frequency of ESTs varied greatly from 1 to 54 per UGT gene model. Among the various tissue types, flower (FL, 18.46%) and seed coat at torpedo stage (TC, 15.69%) had the largest number of highly expressed genes, while globular embryo (GE) stage had the lowest (2, 0.61%) number of expressed genes. The highest number of ESTs (91) were mapped to 13 sequences of group G, followed by 69 ESTs mapping to 15 members of group E. On the contrary, only one EST was mapped to a single group N member. On an average, the highest of 7.00 ESTs were mapped per UGT sequence of family G, followed by 4.60 ESTs per gene of family E. The percentage of the genes expressed per phylogenetic group or family varied from 28% to 100% (Additional file 7). Among all the genes expressed, LuUGT85Q2 and LuUGT74S1 showed the highest expression in flower (FL) and seed coat at torpedo stage (TC), respectively (Additional file 7). Expression analysis of flax UGT genes using microarray data In addition to the sequence based expression analysis method, we also used publicly available microarray data (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21868) under the platform GSE21868, which profiles expression patterns for various flax tissues and seed developmental stages, viz., roots (R), leaves (L), stem outer tissues: vegetative stage (SOV), stem outer tissues: green capsule stage (SOGC), stem inner tissues: vegetative stage (SIV), stem inner tissues: green capsule stage (SIGC), seeds: 10–15 days after flowering (DAF) (S1), seeds: 20–30 DAF (S2) and seeds: 40–50 DAF (S3) [14]. We used the Robust Multichip Average (RMA) -normalized, averaged gene-level log2 values for expression evidence