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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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RT-qPCR expression profile of 10 selected flax UGT genes in 12 different tissue types. Tissue types analysed for LuUGT expression include; mature leaves (ML), stem (ST), root (RT), etiolated seedling (ES), flower (FL) and seed developmental stages (4, 8, 12, 16, 22, 30, 48 DAF). These graphs show the relative transcript abundance of each gene in comparison with the reference gene, Linum usitatissimum ETIF5A (GR508912). Expression values are reported as the average of three biological and two technical replicates. Values correspond to the mean and standard error of biological triplicates.
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Figure 4: RT-qPCR expression profile of 10 selected flax UGT genes in 12 different tissue types. Tissue types analysed for LuUGT expression include; mature leaves (ML), stem (ST), root (RT), etiolated seedling (ES), flower (FL) and seed developmental stages (4, 8, 12, 16, 22, 30, 48 DAF). These graphs show the relative transcript abundance of each gene in comparison with the reference gene, Linum usitatissimum ETIF5A (GR508912). Expression values are reported as the average of three biological and two technical replicates. Values correspond to the mean and standard error of biological triplicates.

Mentions: Relative transcript abundance of 10 flax UGT genes was profiled and is graphically represented in Figure 4. All the selected genes had EST expression evidence and covered six phylogenetic groups. The LuUGT71M1 transcript was detected in mature leaves, stem, etiolated seedling and 48 DAF; however, the relative expression level compared to other UGT genes was very low. LuUGT94G1 expressed constitutively in almost all tissues types; specifically it showed maximum expression in stem. Its expression was also supported by ESTs from stem peel library. LuUGT72N1 expressed in flower, 4 and 8 DAF with peak at 4 DAF. LuUGT85Q2 had 54 ESTs mapped from flower EST library and RT-qPCR analysis confirmed its high expression in flower. Expression of LuUGT89B3 was observed in later stages of seed development viz. 30 and 48 DAF and supported by two EST clones identified in torpedo seed coat stage. LuUGT72M2 expressed in mature leaves, flowers and early seed developmental stages whereas LuUGT72R1 and LuUGT712B1 were highly expressed in various seed developmental stages. LuUGT85Q1 belonged to family 85 which is known to be involved in glycosylation of cyanogenic compounds [19]. The abundance of cyanogenic compounds and higher 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, secoisolariciresinol 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 indicating its putative in planta function as secoisolariciresinol glycosyltransferase. Expression profiles of the 10 selected genes analyzed using RT-qPCR, matched well with the digital expression results.


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)

RT-qPCR expression profile of 10 selected flax UGT genes in 12 different tissue types. Tissue types analysed for LuUGT expression include; mature leaves (ML), stem (ST), root (RT), etiolated seedling (ES), flower (FL) and seed developmental stages (4, 8, 12, 16, 22, 30, 48 DAF). These graphs show the relative transcript abundance of each gene in comparison with the reference gene, Linum usitatissimum ETIF5A (GR508912). Expression values are reported as the average of three biological and two technical replicates. Values correspond to the mean and standard error of biological triplicates.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: RT-qPCR expression profile of 10 selected flax UGT genes in 12 different tissue types. Tissue types analysed for LuUGT expression include; mature leaves (ML), stem (ST), root (RT), etiolated seedling (ES), flower (FL) and seed developmental stages (4, 8, 12, 16, 22, 30, 48 DAF). These graphs show the relative transcript abundance of each gene in comparison with the reference gene, Linum usitatissimum ETIF5A (GR508912). Expression values are reported as the average of three biological and two technical replicates. Values correspond to the mean and standard error of biological triplicates.
Mentions: Relative transcript abundance of 10 flax UGT genes was profiled and is graphically represented in Figure 4. All the selected genes had EST expression evidence and covered six phylogenetic groups. The LuUGT71M1 transcript was detected in mature leaves, stem, etiolated seedling and 48 DAF; however, the relative expression level compared to other UGT genes was very low. LuUGT94G1 expressed constitutively in almost all tissues types; specifically it showed maximum expression in stem. Its expression was also supported by ESTs from stem peel library. LuUGT72N1 expressed in flower, 4 and 8 DAF with peak at 4 DAF. LuUGT85Q2 had 54 ESTs mapped from flower EST library and RT-qPCR analysis confirmed its high expression in flower. Expression of LuUGT89B3 was observed in later stages of seed development viz. 30 and 48 DAF and supported by two EST clones identified in torpedo seed coat stage. LuUGT72M2 expressed in mature leaves, flowers and early seed developmental stages whereas LuUGT72R1 and LuUGT712B1 were highly expressed in various seed developmental stages. LuUGT85Q1 belonged to family 85 which is known to be involved in glycosylation of cyanogenic compounds [19]. The abundance of cyanogenic compounds and higher 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, secoisolariciresinol 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 indicating its putative in planta function as secoisolariciresinol glycosyltransferase. Expression profiles of the 10 selected genes analyzed using RT-qPCR, matched well with the digital expression results.

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