TreeBASE Search-Citation for study 17087

@ARTICLE{TreeBASE2Ref24178, author = {Hwan Su Hwang and Hyoshin Lee and Yong Eui Choi}, title = {Transcriptomic analysis of Siberian ginseng (Eleutherococcus senticosus) to discover genes involved in saponin biosynthesis}, year = {2015}, keywords = {Cytochrome P450, UDP-glycosyltransferase, saponin, transcriptome analysis, de novo sequencing, next-generation sequencing, Eleutherococcus senticosus}, doi = {}, url = {http://}, pmid = {}, journal = {BioMed Central Genomics}, volume = {}, number = {}, pages = {}, abstract = {Background Eleutherococcus senticosus, Siberian ginseng, is a highly valued woody medicinal plant belonging to the family Araliaceae. E. senticosus produces a rich variety of saponins such as oleanane-type, noroleanane-type, 29-hydroxyoleanan-type, and lupane-type saponins. Genomic or transcriptomic approaches have not been used to investigate the saponin biosynthetic pathway in this plant. Result In this study, de novo sequencing was performed to select candidate genes involved in the saponin biosynthetic pathway. A half-plate 454 pyrosequencing run produced 627,923 high-quality reads with an average sequence length of 422 bases. De novo assembly generated 72,811 unique sequences, including 15,217 contigs and 57,594 singletons. Approximately 48,300 (66.3%) unique sequences were annotated using BLAST similarity searches. All of the mevalonate pathway genes for saponin biosynthesis starting from acetyl-CoA were isolated. Moreover, 206 reads of cytochrome P450 (CYP) and 145 reads of uridine diphosphate glycosyltransferase (UGT) sequences were isolated. Based on methyl jasmonate (MeJA) treatment and real-time PCR (qPCR) analysis, 3 CYPs and 3 UGTs were finally selected as candidate genes 1 involved in the saponin biosynthetic pathway. Conclusions The identified sequences associated with saponin biosynthesis will facilitate the study of the functional genomics of saponin biosynthesis and genetic engineering of E. senticosus.} }

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Citation for Study 17087

Citation title: "Transcriptomic analysis of Siberian ginseng (Eleutherococcus senticosus) to discover genes involved in saponin biosynthesis".

Study name: "Transcriptomic analysis of Siberian ginseng (Eleutherococcus senticosus) to discover genes involved in saponin biosynthesis".

This study is part of submission 17087 (Status: Published).

Citation

Hwang H., Lee H., & Choi Y. 2015. Transcriptomic analysis of Siberian ginseng (Eleutherococcus senticosus) to discover genes involved in saponin biosynthesis. BioMed Central Genomics, .

Authors

Hwang H. (submitter) 821039963360
Lee H.
Choi Y.

Abstract

Background Eleutherococcus senticosus, Siberian ginseng, is a highly valued woody medicinal plant belonging to the family Araliaceae. E. senticosus produces a rich variety of saponins such as oleanane-type, noroleanane-type, 29-hydroxyoleanan-type, and lupane-type saponins. Genomic or transcriptomic approaches have not been used to investigate the saponin biosynthetic pathway in this plant. Result In this study, de novo sequencing was performed to select candidate genes involved in the saponin biosynthetic pathway. A half-plate 454 pyrosequencing run produced 627,923 high-quality reads with an average sequence length of 422 bases. De novo assembly generated 72,811 unique sequences, including 15,217 contigs and 57,594 singletons. Approximately 48,300 (66.3%) unique sequences were annotated using BLAST similarity searches. All of the mevalonate pathway genes for saponin biosynthesis starting from acetyl-CoA were isolated. Moreover, 206 reads of cytochrome P450 (CYP) and 145 reads of uridine diphosphate glycosyltransferase (UGT) sequences were isolated. Based on methyl jasmonate (MeJA) treatment and real-time PCR (qPCR) analysis, 3 CYPs and 3 UGTs were finally selected as candidate genes 1 involved in the saponin biosynthetic pathway. Conclusions The identified sequences associated with saponin biosynthesis will facilitate the study of the functional genomics of saponin biosynthesis and genetic engineering of E. senticosus.

Keywords

Cytochrome P450, UDP-glycosyltransferase, saponin, transcriptome analysis, de novo sequencing, next-generation sequencing, Eleutherococcus senticosus

External links

About this resource

Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S17087
Other versions: Nexus NeXML

Show BibTeX reference

		@ARTICLE{TreeBASE2Ref24178,
	 author = {Hwan Su  Hwang and Hyoshin  Lee and Yong Eui  Choi},
	 title = {Transcriptomic analysis of Siberian ginseng (Eleutherococcus senticosus) to discover genes involved in saponin biosynthesis},
	 year = {2015},
	 keywords = {Cytochrome P450, UDP-glycosyltransferase, saponin, transcriptome analysis, de novo sequencing, next-generation sequencing, Eleutherococcus senticosus},
	 doi = {},
	 url = {http://},
	 pmid = {},
	 journal = {BioMed Central Genomics},
	 volume = {},
	 number = {},
	 pages = {},
	 abstract = {Background
Eleutherococcus senticosus, Siberian ginseng, is a highly valued woody medicinal plant belonging to the family Araliaceae. E. senticosus produces a rich variety of saponins such as oleanane-type, noroleanane-type, 29-hydroxyoleanan-type, and lupane-type saponins. Genomic or transcriptomic approaches have not been used to investigate the saponin biosynthetic pathway in this plant.

Result
In this study, de novo sequencing was performed to select candidate genes involved in the saponin biosynthetic pathway. A half-plate 454 pyrosequencing run produced 627,923 high-quality reads with an average sequence length of 422 bases. De novo assembly generated 72,811 unique sequences, including 15,217 contigs and 57,594 singletons. Approximately 48,300 (66.3%) unique sequences were annotated using BLAST similarity searches. All of the mevalonate pathway genes for saponin biosynthesis starting from acetyl-CoA were isolated. Moreover, 206 reads of cytochrome P450 (CYP) and 145 reads of uridine diphosphate glycosyltransferase (UGT) sequences were isolated. Based on methyl jasmonate (MeJA) treatment and real-time PCR (qPCR) analysis, 3 CYPs and 3 UGTs were finally selected as candidate genes 1 involved in the saponin biosynthetic pathway.

Conclusions
The identified sequences associated with saponin biosynthesis will facilitate the study of the functional genomics of saponin biosynthesis and genetic engineering of E. senticosus.}
}

Show RIS reference

TY - JOUR
ID - 24178
AU - Hwang,Hwan Su
AU - Lee,Hyoshin
AU - Choi,Yong Eui
T1 - Transcriptomic analysis of Siberian ginseng (Eleutherococcus senticosus) to discover genes involved in saponin biosynthesis
PY - 2015
KW - Cytochrome P450
KW - UDP-glycosyltransferase
KW - saponin
KW - transcriptome analysis
KW - de novo sequencing
KW - next-generation sequencing
KW - Eleutherococcus senticosus
UR - http://dx.doi.org/
N2 - Background
Eleutherococcus senticosus, Siberian ginseng, is a highly valued woody medicinal plant belonging to the family Araliaceae. E. senticosus produces a rich variety of saponins such as oleanane-type, noroleanane-type, 29-hydroxyoleanan-type, and lupane-type saponins. Genomic or transcriptomic approaches have not been used to investigate the saponin biosynthetic pathway in this plant.

Result
In this study, de novo sequencing was performed to select candidate genes involved in the saponin biosynthetic pathway. A half-plate 454 pyrosequencing run produced 627,923 high-quality reads with an average sequence length of 422 bases. De novo assembly generated 72,811 unique sequences, including 15,217 contigs and 57,594 singletons. Approximately 48,300 (66.3%) unique sequences were annotated using BLAST similarity searches. All of the mevalonate pathway genes for saponin biosynthesis starting from acetyl-CoA were isolated. Moreover, 206 reads of cytochrome P450 (CYP) and 145 reads of uridine diphosphate glycosyltransferase (UGT) sequences were isolated. Based on methyl jasmonate (MeJA) treatment and real-time PCR (qPCR) analysis, 3 CYPs and 3 UGTs were finally selected as candidate genes 1 involved in the saponin biosynthetic pathway.

Conclusions
The identified sequences associated with saponin biosynthesis will facilitate the study of the functional genomics of saponin biosynthesis and genetic engineering of E. senticosus.
L3 -
JF - BioMed Central Genomics
VL -
IS -
ER -