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Phylogenomic analysis of UDP glycosyltransferase 1 multigene family in Linum usitatissimum identified genes with varied expression patterns.

Barvkar VT, Pardeshi VC, Kale SM, Kadoo NY, Gupta VS - BMC Genomics (2012)

Bottom Line: The RT-qPCR results of 10 selected genes were also coherent with the digital expression analysis.Flax has a large number of UGT genes including few flax diverged ones.This study would facilitate precise selection of candidate genes and their further characterization of substrate specificities and in planta functions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Plant Molecular Biology Group, Biochemical Sciences Division, National Chemical Laboratory, Pune, India.

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.

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Phylogenetic analysis of theLinum usitatissimumUGT family genes. The tree was derived by neighbour‒joining distance analysis of alignable regions comprising ~60% of the UGT sequences using MEGA5. Bootstrap values over 60% are indicated at the nodes, with the number on the left for neighbour-joining and right for parsimony methods. Hypothetical positions of intron gain and loss are indicated by dots followed by intron number and it is assumed that introns 3 and 4 were gained prior to diversification of flax UGTs (see Figure 2). Postulated intron gains are indicated by blue dots and intron losses by red dots. Eighteen Arabidopsis and one Sesame UGT sequences from each UGT family were included in the analysis (Accession numbers given in Additional file 2).
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Figure 1: Phylogenetic analysis of theLinum usitatissimumUGT family genes. The tree was derived by neighbour‒joining distance analysis of alignable regions comprising ~60% of the UGT sequences using MEGA5. Bootstrap values over 60% are indicated at the nodes, with the number on the left for neighbour-joining and right for parsimony methods. Hypothetical positions of intron gain and loss are indicated by dots followed by intron number and it is assumed that introns 3 and 4 were gained prior to diversification of flax UGTs (see Figure 2). Postulated intron gains are indicated by blue dots and intron losses by red dots. Eighteen Arabidopsis and one Sesame UGT sequences from each UGT family were included in the analysis (Accession numbers given in Additional file 2).

Mentions: 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 construct 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).


Phylogenomic analysis of UDP glycosyltransferase 1 multigene family in Linum usitatissimum identified genes with varied expression patterns.

Barvkar VT, Pardeshi VC, Kale SM, Kadoo NY, Gupta VS - BMC Genomics (2012)

Phylogenetic analysis of theLinum usitatissimumUGT family genes. The tree was derived by neighbour‒joining distance analysis of alignable regions comprising ~60% of the UGT sequences using MEGA5. Bootstrap values over 60% are indicated at the nodes, with the number on the left for neighbour-joining and right for parsimony methods. Hypothetical positions of intron gain and loss are indicated by dots followed by intron number and it is assumed that introns 3 and 4 were gained prior to diversification of flax UGTs (see Figure 2). Postulated intron gains are indicated by blue dots and intron losses by red dots. Eighteen Arabidopsis and one Sesame UGT sequences from each UGT family were included in the analysis (Accession numbers given in Additional file 2).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3412749&req=5

Figure 1: Phylogenetic analysis of theLinum usitatissimumUGT family genes. The tree was derived by neighbour‒joining distance analysis of alignable regions comprising ~60% of the UGT sequences using MEGA5. Bootstrap values over 60% are indicated at the nodes, with the number on the left for neighbour-joining and right for parsimony methods. Hypothetical positions of intron gain and loss are indicated by dots followed by intron number and it is assumed that introns 3 and 4 were gained prior to diversification of flax UGTs (see Figure 2). Postulated intron gains are indicated by blue dots and intron losses by red dots. Eighteen Arabidopsis and one Sesame UGT sequences from each UGT family were included in the analysis (Accession numbers given in Additional file 2).
Mentions: 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 construct 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).

Bottom Line: The RT-qPCR results of 10 selected genes were also coherent with the digital expression analysis.Flax has a large number of UGT genes including few flax diverged ones.This study would facilitate precise selection of candidate genes and their further characterization of substrate specificities and in planta functions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Plant Molecular Biology Group, Biochemical Sciences Division, National Chemical Laboratory, Pune, India.

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.

Show MeSH
Related in: MedlinePlus