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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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Expression levels for flax UGT genes in various tissues by microarray analysis. The RMA‒normalized, average log2 signal values of flax UGTs in various tissues and seed developmental stages (listed at the top of heat map) were used for construction of the heat map. The left side of the heat map shows hierarchical clustering based on Pearson correlation matrix. The colour scale (representing log2 signal values) is shown at the top. Microarray data from 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), leaves (L), roots (R), seeds, 10–15 DAF (S1), seeds, 20–30 DAF (S2) and seeds, 40–50 DAF (S3) were used for constructing the expression heat map.
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Figure 3: Expression levels for flax UGT genes in various tissues by microarray analysis. The RMA‒normalized, average log2 signal values of flax UGTs in various tissues and seed developmental stages (listed at the top of heat map) were used for construction of the heat map. The left side of the heat map shows hierarchical clustering based on Pearson correlation matrix. The colour scale (representing log2 signal values) is shown at the top. Microarray data from 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), leaves (L), roots (R), seeds, 10–15 DAF (S1), seeds, 20–30 DAF (S2) and seeds, 40–50 DAF (S3) were used for constructing the expression heat map.

Mentions: 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 of UGTs to construct a heat map (Figure 3). Hierarchical clustering with Pearson correlation matrix highlighted co-expression of specific gene family members in specific tissue types. Only 60 of the 137 (43.79%) flax UGTs represented on the array showed expression evidence (Additional file 7). Three genes were highly expressed in seed stages S2 and S3 (averaged gene-level log2 value: LuUGT85R2 (11.11 and 11.30), LuUGT709E2 (10.57 and 10.76), and LuUGT709E3 (10.57 and 10.76), respectively; while one gene (LuUGT85Q3, averaged gene-level log2 value: 11.53) showed the highest expression in leaf tissue (Figure 3). The number of genes having higher expression in different tissues (averaged gene-level log2 values >6.96) varied from 14 (S1) to 24 (SOGC) (Additional file 7). Among the different tissues, SOGC had the largest number of highly expressed genes, while S3 had the lowest (23%) (Additional file 7). Surprisingly, the two contrasting varieties, Drakkar and Belinka did not show any difference in the expression of these 60 UGTs (Figure 3).


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)

Expression levels for flax UGT genes in various tissues by microarray analysis. The RMA‒normalized, average log2 signal values of flax UGTs in various tissues and seed developmental stages (listed at the top of heat map) were used for construction of the heat map. The left side of the heat map shows hierarchical clustering based on Pearson correlation matrix. The colour scale (representing log2 signal values) is shown at the top. Microarray data from 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), leaves (L), roots (R), seeds, 10–15 DAF (S1), seeds, 20–30 DAF (S2) and seeds, 40–50 DAF (S3) were used for constructing the expression heat map.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Expression levels for flax UGT genes in various tissues by microarray analysis. The RMA‒normalized, average log2 signal values of flax UGTs in various tissues and seed developmental stages (listed at the top of heat map) were used for construction of the heat map. The left side of the heat map shows hierarchical clustering based on Pearson correlation matrix. The colour scale (representing log2 signal values) is shown at the top. Microarray data from 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), leaves (L), roots (R), seeds, 10–15 DAF (S1), seeds, 20–30 DAF (S2) and seeds, 40–50 DAF (S3) were used for constructing the expression heat map.
Mentions: 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 of UGTs to construct a heat map (Figure 3). Hierarchical clustering with Pearson correlation matrix highlighted co-expression of specific gene family members in specific tissue types. Only 60 of the 137 (43.79%) flax UGTs represented on the array showed expression evidence (Additional file 7). Three genes were highly expressed in seed stages S2 and S3 (averaged gene-level log2 value: LuUGT85R2 (11.11 and 11.30), LuUGT709E2 (10.57 and 10.76), and LuUGT709E3 (10.57 and 10.76), respectively; while one gene (LuUGT85Q3, averaged gene-level log2 value: 11.53) showed the highest expression in leaf tissue (Figure 3). The number of genes having higher expression in different tissues (averaged gene-level log2 values >6.96) varied from 14 (S1) to 24 (SOGC) (Additional file 7). Among the different tissues, SOGC had the largest number of highly expressed genes, while S3 had the lowest (23%) (Additional file 7). Surprisingly, the two contrasting varieties, Drakkar and Belinka did not show any difference in the expression of these 60 UGTs (Figure 3).

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