Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi

R.A. Cacho, Y. Tang, Heng Chooi

Research output: Contribution to journalArticle

34 Citations (Scopus)

Abstract

© 2015 Cacho, Tang and Chooi. Genomics has revolutionized the research on fungal secondary metabolite (SM) biosynthesis. To elucidate the molecular and enzymatic mechanisms underlying the biosynthesis of a specific SM compound, the important first step is often to find the genes that responsible for its synthesis. The accessibility to fungal genome sequences allows the bypass of the cumbersome traditional library construction and screening approach. The advance in next-generation sequencing (NGS) technologies have further improved the speed and reduced the cost of microbial genome sequencing in the past few years, which has accelerated the research in this field. Here, we will present an example work flow for identifying the gene cluster encoding the biosynthesis of SMs of interest using an NGS approach. We will also review the different strategies that can be employed to pinpoint the targeted gene clusters rapidly by giving several examples stemming from our work.
Original languageEnglish
Pages (from-to)1-16
JournalFrontiers in Microbiology
Volume5
DOIs
Publication statusPublished - 2015

Fingerprint

Multigene Family
Fungi
Fungal Genome
Microbial Genome
Workflow
Genomics
Research
Libraries
Technology
Costs and Cost Analysis
Genes

Cite this

@article{a4454a257e7f451b98fd7e8853f340ee,
title = "Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi",
abstract = "{\circledC} 2015 Cacho, Tang and Chooi. Genomics has revolutionized the research on fungal secondary metabolite (SM) biosynthesis. To elucidate the molecular and enzymatic mechanisms underlying the biosynthesis of a specific SM compound, the important first step is often to find the genes that responsible for its synthesis. The accessibility to fungal genome sequences allows the bypass of the cumbersome traditional library construction and screening approach. The advance in next-generation sequencing (NGS) technologies have further improved the speed and reduced the cost of microbial genome sequencing in the past few years, which has accelerated the research in this field. Here, we will present an example work flow for identifying the gene cluster encoding the biosynthesis of SMs of interest using an NGS approach. We will also review the different strategies that can be employed to pinpoint the targeted gene clusters rapidly by giving several examples stemming from our work.",
author = "R.A. Cacho and Y. Tang and Heng Chooi",
year = "2015",
doi = "10.3389/fmicb.2014.00774",
language = "English",
volume = "5",
pages = "1--16",
journal = "Frontiers in Microbiology",
issn = "1664-302X",
publisher = "Frontiers Media SA",

}

Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi. / Cacho, R.A.; Tang, Y.; Chooi, Heng.

In: Frontiers in Microbiology, Vol. 5, 2015, p. 1-16.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi

AU - Cacho, R.A.

AU - Tang, Y.

AU - Chooi, Heng

PY - 2015

Y1 - 2015

N2 - © 2015 Cacho, Tang and Chooi. Genomics has revolutionized the research on fungal secondary metabolite (SM) biosynthesis. To elucidate the molecular and enzymatic mechanisms underlying the biosynthesis of a specific SM compound, the important first step is often to find the genes that responsible for its synthesis. The accessibility to fungal genome sequences allows the bypass of the cumbersome traditional library construction and screening approach. The advance in next-generation sequencing (NGS) technologies have further improved the speed and reduced the cost of microbial genome sequencing in the past few years, which has accelerated the research in this field. Here, we will present an example work flow for identifying the gene cluster encoding the biosynthesis of SMs of interest using an NGS approach. We will also review the different strategies that can be employed to pinpoint the targeted gene clusters rapidly by giving several examples stemming from our work.

AB - © 2015 Cacho, Tang and Chooi. Genomics has revolutionized the research on fungal secondary metabolite (SM) biosynthesis. To elucidate the molecular and enzymatic mechanisms underlying the biosynthesis of a specific SM compound, the important first step is often to find the genes that responsible for its synthesis. The accessibility to fungal genome sequences allows the bypass of the cumbersome traditional library construction and screening approach. The advance in next-generation sequencing (NGS) technologies have further improved the speed and reduced the cost of microbial genome sequencing in the past few years, which has accelerated the research in this field. Here, we will present an example work flow for identifying the gene cluster encoding the biosynthesis of SMs of interest using an NGS approach. We will also review the different strategies that can be employed to pinpoint the targeted gene clusters rapidly by giving several examples stemming from our work.

U2 - 10.3389/fmicb.2014.00774

DO - 10.3389/fmicb.2014.00774

M3 - Article

VL - 5

SP - 1

EP - 16

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

SN - 1664-302X

ER -