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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.


Related in: MedlinePlus

qRT-PCR analysises.qRT-PCRwas performed to validate the 12 differentially expressed unigenes related to terpenoid biosynthesis and/or unsaturated fatty acid metabolisms. The gene names, serial numbers and primer sequences used for qRT-PCR analysis are shown in S8 Table.
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pone.0135724.g006: qRT-PCR analysises.qRT-PCRwas performed to validate the 12 differentially expressed unigenes related to terpenoid biosynthesis and/or unsaturated fatty acid metabolisms. The gene names, serial numbers and primer sequences used for qRT-PCR analysis are shown in S8 Table.

Mentions: To confirm the difference in expression of unigenes detected by RNA-seq, 12 DEGs that were predicted to be coding for key enzymes involved in terpenoid and unsaturated fatty acid metabolic pathways were selected for qRT-PCR validation (S8 Table). As a result, six unigenes exhibited higher expression levels in the bark than those in the leaf, including FabF, ACOT8, ACAD, DXS, HMGR and WuMts1; while the remaining six unigenes, such as FAD7 (a ω-3 fatty acid desaturase) and FAD6 (a ω-6 fatty acid desaturase) showed lower expression levels in the bark than those in the leaf (Fig 6). The data of qRT-PCRs mostly match the results by RNA-seq, which suggests the reliability of the transcriptome database (S8 Table).


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)

qRT-PCR analysises.qRT-PCRwas performed to validate the 12 differentially expressed unigenes related to terpenoid biosynthesis and/or unsaturated fatty acid metabolisms. The gene names, serial numbers and primer sequences used for qRT-PCR analysis are shown in S8 Table.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4549110&req=5

pone.0135724.g006: qRT-PCR analysises.qRT-PCRwas performed to validate the 12 differentially expressed unigenes related to terpenoid biosynthesis and/or unsaturated fatty acid metabolisms. The gene names, serial numbers and primer sequences used for qRT-PCR analysis are shown in S8 Table.
Mentions: To confirm the difference in expression of unigenes detected by RNA-seq, 12 DEGs that were predicted to be coding for key enzymes involved in terpenoid and unsaturated fatty acid metabolic pathways were selected for qRT-PCR validation (S8 Table). As a result, six unigenes exhibited higher expression levels in the bark than those in the leaf, including FabF, ACOT8, ACAD, DXS, HMGR and WuMts1; while the remaining six unigenes, such as FAD7 (a ω-3 fatty acid desaturase) and FAD6 (a ω-6 fatty acid desaturase) showed lower expression levels in the bark than those in the leaf (Fig 6). The data of qRT-PCRs mostly match the results by RNA-seq, which suggests the reliability of the transcriptome database (S8 Table).

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.


Related in: MedlinePlus