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De Novo Transcriptome Analysis of Warburgia ugandensis to Identify Genes Involved in Terpenoids and Unsaturated Fatty Acids Biosynthesis.

Wang X, Zhou C, Yang X, Miao D, Zhang Y - PLoS ONE (2015)

Bottom Line: In addition, the expression of 12 DEGs with putative roles in terpenoid and unsaturated fatty acid metabolic pathways was confirmed by qRT-PCRs, which was consistent with the data of the RNA-sequencing.In conclusion, we constructed a comprehensive transcriptome dataset derived from the bark and leaf of W. ugandensis, which forms the basis for functional genomics studies on this plant species.Particularly, the comparative analysis of the transcriptome data between the bark and leaf will provide critical clues to reveal the regulatory mechanisms underlying the biosynthesis of terpenoids and PUFAs in W. ugandensis.

View Article: PubMed Central - PubMed

Affiliation: CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.

ABSTRACT
The bark of Warburgia ugandensis (Canellaceae family) has been used as a medicinal source for a long history in many African countries. The presence of diverse terpenoids and abundant polyunsaturated fatty acids (PUFAs) in this organ contributes to its broad range of pharmacological properties. Despite its medicinal and economic importance, the knowledge on the biosynthesis of terpenoid and unsaturated fatty acid in W. ugandensis bark remains largely unknown. Therefore, it is necessary to construct a genomic and/or transcriptomic database for the functional genomics study on W. ugandensis. The chemical profiles of terpenoids and fatty acids between the bark and leaves of W. ugandensis were compared by gas chromatography-mass spectrometry (GC-MS) analysis. Meanwhile, the transcriptome database derived from both tissues was created using Illumina sequencing technology. In total, about 17.1 G clean nucleotides were obtained, and de novo assembled into 72,591 unigenes, of which about 38.06% can be aligned to the NCBI non-redundant protein database. Many candidate genes in the biosynthetic pathways of terpenoids and unsaturated fatty acids were identified, including 14 unigenes for terpene synthases. Furthermore, 2,324 unigenes were discovered to be differentially expressed between both tissues; the functions of those differentially expressed genes (DEGs) were predicted by gene ontology enrichment and metabolic pathway enrichment analyses. In addition, the expression of 12 DEGs with putative roles in terpenoid and unsaturated fatty acid metabolic pathways was confirmed by qRT-PCRs, which was consistent with the data of the RNA-sequencing. In conclusion, we constructed a comprehensive transcriptome dataset derived from the bark and leaf of W. ugandensis, which forms the basis for functional genomics studies on this plant species. Particularly, the comparative analysis of the transcriptome data between the bark and leaf will provide critical clues to reveal the regulatory mechanisms underlying the biosynthesis of terpenoids and PUFAs in W. ugandensis.

No MeSH data available.


Putative structural genes involved in terpenoid backbone biosynthesis pathway.The values in the bracket indicate the number of unigenes in the corresponding gene families. ACCT, acetyl-CoA C-acetyltransferase; HMGS, hydroxymethylglutaryl-CoA synthase; HMGR, hydroxymethylglutaryl-CoA reductase; MVK, mevalonate kinase; PMK, phosphomevalonate kinase; MVD, mevalonate diphosphate decarboxylase; DXS, 1-deoxy-D-xylulose-5-phosphate synthase; DXR, 1-deoxy-D-xylulose-5-phosphate reductoisomerase; MCT, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase; CMK, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; MECPS, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; HDR, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; HDS, (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase; IDI, isopentenyl-diphosphate delta-isomerase; GPPS, geranyl diphosphate synthase; FPPS, farnesyl diphosphate synthase; STS, Sesquiterpenoid synthase; MTS, Monoterpenoid synthase.
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pone.0135724.g004: Putative structural genes involved in terpenoid backbone biosynthesis pathway.The values in the bracket indicate the number of unigenes in the corresponding gene families. ACCT, acetyl-CoA C-acetyltransferase; HMGS, hydroxymethylglutaryl-CoA synthase; HMGR, hydroxymethylglutaryl-CoA reductase; MVK, mevalonate kinase; PMK, phosphomevalonate kinase; MVD, mevalonate diphosphate decarboxylase; DXS, 1-deoxy-D-xylulose-5-phosphate synthase; DXR, 1-deoxy-D-xylulose-5-phosphate reductoisomerase; MCT, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase; CMK, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; MECPS, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; HDR, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; HDS, (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase; IDI, isopentenyl-diphosphate delta-isomerase; GPPS, geranyl diphosphate synthase; FPPS, farnesyl diphosphate synthase; STS, Sesquiterpenoid synthase; MTS, Monoterpenoid synthase.

Mentions: Although mono- and sesqui-terpenoids were detected in W. ugandensis, the structural genes involved in these biosynthetic pathways have been largely unknown so far. Analysis of the transcriptome data allowed us to identify 17 unigenes coding for four enzymes in the mevalonate pathway and 20 unigenes for five enzymes in the MEP pathway, which synthesizes the common precursor isopentenyl diphosphate (IPP) for downstream terpenoid pathways (Fig 4). Like those in other organisms, the structural genes for upstream terpenoid pathways are presented as multi-members in W. ugandensis. For example, six unigenes were predicted to code for hydroxymethylglutaryl-CoA reductase (HMGR), which is the first committed enzyme in the mevalonate pathway to form mevalonate (S2 Table); six unigenes were for 1-deoxy-D-xylulose-5-phosphate synthase (DXS) that catalyzes the conversion of pyruvate and D-glyceraldehyde 3-phosphate into 1-deoxy-D-xylulose-5-phosphate (DOXP) in the first step in the MEP pathway; two unigenes were for isopentenyl-diphosphate delta-isomerase (IDI), which catalyzes the isomerization of isopentenyl diphosphate to dimethylallyl diphosphate; seven unigenes were annotated to encode prenyltransferases in terpenoid pathways, of which three unigenes were for GPPSs and four unigenes for FPPSs.


De Novo Transcriptome Analysis of Warburgia ugandensis to Identify Genes Involved in Terpenoids and Unsaturated Fatty Acids Biosynthesis.

Wang X, Zhou C, Yang X, Miao D, Zhang Y - PLoS ONE (2015)

Putative structural genes involved in terpenoid backbone biosynthesis pathway.The values in the bracket indicate the number of unigenes in the corresponding gene families. ACCT, acetyl-CoA C-acetyltransferase; HMGS, hydroxymethylglutaryl-CoA synthase; HMGR, hydroxymethylglutaryl-CoA reductase; MVK, mevalonate kinase; PMK, phosphomevalonate kinase; MVD, mevalonate diphosphate decarboxylase; DXS, 1-deoxy-D-xylulose-5-phosphate synthase; DXR, 1-deoxy-D-xylulose-5-phosphate reductoisomerase; MCT, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase; CMK, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; MECPS, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; HDR, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; HDS, (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase; IDI, isopentenyl-diphosphate delta-isomerase; GPPS, geranyl diphosphate synthase; FPPS, farnesyl diphosphate synthase; STS, Sesquiterpenoid synthase; MTS, Monoterpenoid synthase.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4549110&req=5

pone.0135724.g004: Putative structural genes involved in terpenoid backbone biosynthesis pathway.The values in the bracket indicate the number of unigenes in the corresponding gene families. ACCT, acetyl-CoA C-acetyltransferase; HMGS, hydroxymethylglutaryl-CoA synthase; HMGR, hydroxymethylglutaryl-CoA reductase; MVK, mevalonate kinase; PMK, phosphomevalonate kinase; MVD, mevalonate diphosphate decarboxylase; DXS, 1-deoxy-D-xylulose-5-phosphate synthase; DXR, 1-deoxy-D-xylulose-5-phosphate reductoisomerase; MCT, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase; CMK, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; MECPS, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; HDR, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; HDS, (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase; IDI, isopentenyl-diphosphate delta-isomerase; GPPS, geranyl diphosphate synthase; FPPS, farnesyl diphosphate synthase; STS, Sesquiterpenoid synthase; MTS, Monoterpenoid synthase.
Mentions: Although mono- and sesqui-terpenoids were detected in W. ugandensis, the structural genes involved in these biosynthetic pathways have been largely unknown so far. Analysis of the transcriptome data allowed us to identify 17 unigenes coding for four enzymes in the mevalonate pathway and 20 unigenes for five enzymes in the MEP pathway, which synthesizes the common precursor isopentenyl diphosphate (IPP) for downstream terpenoid pathways (Fig 4). Like those in other organisms, the structural genes for upstream terpenoid pathways are presented as multi-members in W. ugandensis. For example, six unigenes were predicted to code for hydroxymethylglutaryl-CoA reductase (HMGR), which is the first committed enzyme in the mevalonate pathway to form mevalonate (S2 Table); six unigenes were for 1-deoxy-D-xylulose-5-phosphate synthase (DXS) that catalyzes the conversion of pyruvate and D-glyceraldehyde 3-phosphate into 1-deoxy-D-xylulose-5-phosphate (DOXP) in the first step in the MEP pathway; two unigenes were for isopentenyl-diphosphate delta-isomerase (IDI), which catalyzes the isomerization of isopentenyl diphosphate to dimethylallyl diphosphate; seven unigenes were annotated to encode prenyltransferases in terpenoid pathways, of which three unigenes were for GPPSs and four unigenes for FPPSs.

Bottom Line: In addition, the expression of 12 DEGs with putative roles in terpenoid and unsaturated fatty acid metabolic pathways was confirmed by qRT-PCRs, which was consistent with the data of the RNA-sequencing.In conclusion, we constructed a comprehensive transcriptome dataset derived from the bark and leaf of W. ugandensis, which forms the basis for functional genomics studies on this plant species.Particularly, the comparative analysis of the transcriptome data between the bark and leaf will provide critical clues to reveal the regulatory mechanisms underlying the biosynthesis of terpenoids and PUFAs in W. ugandensis.

View Article: PubMed Central - PubMed

Affiliation: CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.

ABSTRACT
The bark of Warburgia ugandensis (Canellaceae family) has been used as a medicinal source for a long history in many African countries. The presence of diverse terpenoids and abundant polyunsaturated fatty acids (PUFAs) in this organ contributes to its broad range of pharmacological properties. Despite its medicinal and economic importance, the knowledge on the biosynthesis of terpenoid and unsaturated fatty acid in W. ugandensis bark remains largely unknown. Therefore, it is necessary to construct a genomic and/or transcriptomic database for the functional genomics study on W. ugandensis. The chemical profiles of terpenoids and fatty acids between the bark and leaves of W. ugandensis were compared by gas chromatography-mass spectrometry (GC-MS) analysis. Meanwhile, the transcriptome database derived from both tissues was created using Illumina sequencing technology. In total, about 17.1 G clean nucleotides were obtained, and de novo assembled into 72,591 unigenes, of which about 38.06% can be aligned to the NCBI non-redundant protein database. Many candidate genes in the biosynthetic pathways of terpenoids and unsaturated fatty acids were identified, including 14 unigenes for terpene synthases. Furthermore, 2,324 unigenes were discovered to be differentially expressed between both tissues; the functions of those differentially expressed genes (DEGs) were predicted by gene ontology enrichment and metabolic pathway enrichment analyses. In addition, the expression of 12 DEGs with putative roles in terpenoid and unsaturated fatty acid metabolic pathways was confirmed by qRT-PCRs, which was consistent with the data of the RNA-sequencing. In conclusion, we constructed a comprehensive transcriptome dataset derived from the bark and leaf of W. ugandensis, which forms the basis for functional genomics studies on this plant species. Particularly, the comparative analysis of the transcriptome data between the bark and leaf will provide critical clues to reveal the regulatory mechanisms underlying the biosynthesis of terpenoids and PUFAs in W. ugandensis.

No MeSH data available.