publication . Article . 2016

De novo transcriptome sequencing in Monsonia burkeana revealed putative genes for key metabolic pathways involved in tea quality and medicinal value

Woldesemayat, Adugna A.; Ntushelo, Khayalethu; Modise, David M.;
Open Access English
  • Published: 19 Nov 2016 Journal: 3 Biotech, volume 6, issue 2 (issn: 2190-572X, Copyright policy)
  • Publisher: Springer Nature
Abstract
Monsonia (Monsonia burkeana Planch. ex Harv) is one of the most valuable tea and traditional medicinal plants used in Southern Africa. In spite of this, there is no sequence information regarding this plant in literature. To provide understanding of the naturally occurring tea and drug-specific products and the key pathways for the biosynthesis of these molecules, we sequenced the leaf transcriptome using Illumina MiSeq platform and generated 2,590,652 paired-end reads that were assembled de novo into 45,450 high-quality transcripts. Annotation of these transcripts revealed best hits for homology to discover more than 17,800 functional genes and conserved domain...
Subjects
Medical Subject Headings: food and beverages
free text keywords: Biotechnology, Agricultural and Biological Sciences (miscellaneous), Environmental Science (miscellaneous), Homology (biology), Phylogenetic tree, KEGG, Genetics, Gene, Gene family, Sequence assembly, Biology, Transcriptome, Illumina dye sequencing, Original Article, De novo assembly, Monsonia burkeana, Functional annotation, Illumina sequencing, Metabolic pathways
Related Organizations
41 references, page 1 of 3

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Balasundram, N, Sundram, K, Samman, S. Phenolic compounds in plants and agri-industrial by-products: antioxidant activity, occurrence, and potential uses. Food Chem. 2006; 99: 191-203 [OpenAIRE] [DOI]

Boerjan, W, Ralph, J, Baucher, M. Lignin biosynthesis. Annu Rev Plant Biol. 2003; 54: 519-546 [OpenAIRE] [PubMed] [DOI]

Camon, E, Magrane, M, Barrell, D. The gene ontology annotation (GOA) database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res. 2004; 32: D262-D266 [OpenAIRE] [PubMed] [DOI]

Conesa, A, Götz, S, García-Gómez, JM. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005; 21: 3674-3676 [PubMed] [DOI]

Cushnie, TT, Cushnie, B, Lamb, AJ. Alkaloids: an overview of their antibacterial, antibiotic-enhancing and antivirulence activities. Int J Antimicrob Agents. 2014; 44: 377-386 [OpenAIRE] [PubMed] [DOI]

Dajas, F, Juan Andres, A-C, Florencia, A. Neuroprotective actions of flavones and flavonols: mechanisms and relationship to flavonoid structural features. Cent Nerv Syst Agents Med Chem Former Curr Med Chem-Cent Nerv Syst Agents. 2013; 13: 30-35 [DOI]

Du, Z, Zhou, X, Ling, Y. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 2010; 38: W64-W70 [OpenAIRE] [PubMed] [DOI]

Finn, RD, Coggill, P, Eberhardt, RY. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2016; 44: D279-D285 [OpenAIRE] [PubMed] [DOI]

Garg, R, Patel, RK, Tyagi, AK, Jain, M. De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res. 2011; 18: 53-63 [OpenAIRE] [PubMed] [DOI]

Gordon A, Hannon GJ (2010) Fastx-toolkit. http://hannonlab.cshl.edu/fastx_toolkit/index.html

Grabherr, MG, Haas, BJ, Yassour, M. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011; 29: 644-652 [OpenAIRE] [PubMed] [DOI]

Gullo, VP. Discovery of novel natural products with therapeutic potential. 1994

41 references, page 1 of 3
Abstract
Monsonia (Monsonia burkeana Planch. ex Harv) is one of the most valuable tea and traditional medicinal plants used in Southern Africa. In spite of this, there is no sequence information regarding this plant in literature. To provide understanding of the naturally occurring tea and drug-specific products and the key pathways for the biosynthesis of these molecules, we sequenced the leaf transcriptome using Illumina MiSeq platform and generated 2,590,652 paired-end reads that were assembled de novo into 45,450 high-quality transcripts. Annotation of these transcripts revealed best hits for homology to discover more than 17,800 functional genes and conserved domain...
Subjects
Medical Subject Headings: food and beverages
free text keywords: Biotechnology, Agricultural and Biological Sciences (miscellaneous), Environmental Science (miscellaneous), Homology (biology), Phylogenetic tree, KEGG, Genetics, Gene, Gene family, Sequence assembly, Biology, Transcriptome, Illumina dye sequencing, Original Article, De novo assembly, Monsonia burkeana, Functional annotation, Illumina sequencing, Metabolic pathways
Related Organizations
41 references, page 1 of 3

Altschul, SF, Gish, W, Miller, W. Basic local alignment search tool. J Mol Biol. 1990; 215: 403-410 [OpenAIRE] [PubMed] [DOI]

Andrews S (2010) FastQC: A quality control tool for high throughput sequence data. Babraham Bioinform. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Ashburner, M, Ball, CA, Blake, JA. Gene Ontology: tool for the unification of biology. Nat Genet. 2000; 25: 25-29 [OpenAIRE] [PubMed] [DOI]

Balasundram, N, Sundram, K, Samman, S. Phenolic compounds in plants and agri-industrial by-products: antioxidant activity, occurrence, and potential uses. Food Chem. 2006; 99: 191-203 [OpenAIRE] [DOI]

Boerjan, W, Ralph, J, Baucher, M. Lignin biosynthesis. Annu Rev Plant Biol. 2003; 54: 519-546 [OpenAIRE] [PubMed] [DOI]

Camon, E, Magrane, M, Barrell, D. The gene ontology annotation (GOA) database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res. 2004; 32: D262-D266 [OpenAIRE] [PubMed] [DOI]

Conesa, A, Götz, S, García-Gómez, JM. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005; 21: 3674-3676 [PubMed] [DOI]

Cushnie, TT, Cushnie, B, Lamb, AJ. Alkaloids: an overview of their antibacterial, antibiotic-enhancing and antivirulence activities. Int J Antimicrob Agents. 2014; 44: 377-386 [OpenAIRE] [PubMed] [DOI]

Dajas, F, Juan Andres, A-C, Florencia, A. Neuroprotective actions of flavones and flavonols: mechanisms and relationship to flavonoid structural features. Cent Nerv Syst Agents Med Chem Former Curr Med Chem-Cent Nerv Syst Agents. 2013; 13: 30-35 [DOI]

Du, Z, Zhou, X, Ling, Y. agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 2010; 38: W64-W70 [OpenAIRE] [PubMed] [DOI]

Finn, RD, Coggill, P, Eberhardt, RY. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2016; 44: D279-D285 [OpenAIRE] [PubMed] [DOI]

Garg, R, Patel, RK, Tyagi, AK, Jain, M. De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification. DNA Res. 2011; 18: 53-63 [OpenAIRE] [PubMed] [DOI]

Gordon A, Hannon GJ (2010) Fastx-toolkit. http://hannonlab.cshl.edu/fastx_toolkit/index.html

Grabherr, MG, Haas, BJ, Yassour, M. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011; 29: 644-652 [OpenAIRE] [PubMed] [DOI]

Gullo, VP. Discovery of novel natural products with therapeutic potential. 1994

41 references, page 1 of 3
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publication . Article . 2016

De novo transcriptome sequencing in Monsonia burkeana revealed putative genes for key metabolic pathways involved in tea quality and medicinal value

Woldesemayat, Adugna A.; Ntushelo, Khayalethu; Modise, David M.;