Genomic approaches for interrogating the biochemistry of medicinal plant species

Elsa Góngora-Castillo; Greg Fedewa; Yunsoo Yeo; Joe Chappell; Dean Dellapenna; C. Robin Buell

doi:10.1016/B978-0-12-404634-4.00007-3

Genomic approaches for interrogating the biochemistry of medicinal plant species

Elsa Góngora-Castillo, Greg Fedewa, Yunsoo Yeo, Joe Chappell, Dean Dellapenna, C. Robin Buell

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

48 Scopus citations

Abstract

Development of next-generation sequencing, coupled with the advancement of computational methods, has allowed researchers to access the transcriptomes of recalcitrant genomes such as those of medicinal plant species. Through the sequencing of even a few cDNA libraries, a broad representation of the transcriptome of any medicinal plant species can be obtained, providing a robust resource for gene discovery and downstream biochemical pathway discovery. When coupled to estimation of expression abundances in specific tissues from a developmental series, biotic stress, abiotic stress, or elicitor challenge, informative coexpression and differential expression estimates on a whole transcriptome level can be obtained to identify candidates for function discovery.

Original language	English
Title of host publication	Natural Product Biosynthesis by Microorganisms and Plants, Part C
Pages	139-159
Number of pages	21
DOIs	https://doi.org/10.1016/B978-0-12-404634-4.00007-3
State	Published - 2012

Publication series

Name	Methods in Enzymology
Volume	517
ISSN (Print)	0076-6879
ISSN (Electronic)	1557-7988

Bibliographical note

Funding Information:
Funding for medicinal plant transcriptome work was provided by a grant to J. C., D. D. P., and C. R. B. from the National Institute of General Medical Sciences (1RC2GM092521) and from the Michigan State University GREEEN program to C. R. B. (GR11-181).

Funding

Funding for medicinal plant transcriptome work was provided by a grant to J. C., D. D. P., and C. R. B. from the National Institute of General Medical Sciences (1RC2GM092521) and from the Michigan State University GREEEN program to C. R. B. (GR11-181).

Funders	Funder number
National Institute of General Medical Sciences	RC2GM092521
Michigan State University	GR11-181

Keywords

Annotation
Expression abundance
Isoforms
Transcriptome

ASJC Scopus subject areas

Biochemistry
Molecular Biology

Access to Document

10.1016/B978-0-12-404634-4.00007-3

Cite this

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abstract = "Development of next-generation sequencing, coupled with the advancement of computational methods, has allowed researchers to access the transcriptomes of recalcitrant genomes such as those of medicinal plant species. Through the sequencing of even a few cDNA libraries, a broad representation of the transcriptome of any medicinal plant species can be obtained, providing a robust resource for gene discovery and downstream biochemical pathway discovery. When coupled to estimation of expression abundances in specific tissues from a developmental series, biotic stress, abiotic stress, or elicitor challenge, informative coexpression and differential expression estimates on a whole transcriptome level can be obtained to identify candidates for function discovery.",

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note = "Funding Information: Funding for medicinal plant transcriptome work was provided by a grant to J. C., D. D. P., and C. R. B. from the National Institute of General Medical Sciences (1RC2GM092521) and from the Michigan State University GREEEN program to C. R. B. (GR11-181).",

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AU - Fedewa, Greg

AU - Yeo, Yunsoo

AU - Chappell, Joe

AU - Dellapenna, Dean

AU - Buell, C. Robin

N1 - Funding Information: Funding for medicinal plant transcriptome work was provided by a grant to J. C., D. D. P., and C. R. B. from the National Institute of General Medical Sciences (1RC2GM092521) and from the Michigan State University GREEEN program to C. R. B. (GR11-181).

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AB - Development of next-generation sequencing, coupled with the advancement of computational methods, has allowed researchers to access the transcriptomes of recalcitrant genomes such as those of medicinal plant species. Through the sequencing of even a few cDNA libraries, a broad representation of the transcriptome of any medicinal plant species can be obtained, providing a robust resource for gene discovery and downstream biochemical pathway discovery. When coupled to estimation of expression abundances in specific tissues from a developmental series, biotic stress, abiotic stress, or elicitor challenge, informative coexpression and differential expression estimates on a whole transcriptome level can be obtained to identify candidates for function discovery.

KW - Annotation

KW - Expression abundance

KW - Isoforms

KW - Transcriptome

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Genomic approaches for interrogating the biochemistry of medicinal plant species

Abstract

Publication series

Bibliographical note

Funding

Keywords

ASJC Scopus subject areas

Access to Document

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Cite this