Pathway and Gene Discovery from Natural Hosts and Organisms

Jing Ke; Yasuo Yoshikuni

doi:10.1007/978-1-4939-9142-6_1

Pathway and Gene Discovery from Natural Hosts and Organisms

Methods Mol Biol. 2019:1927:1-9. doi: 10.1007/978-1-4939-9142-6_1.

Authors

Jing Ke¹, Yasuo Yoshikuni²

Affiliations

¹ U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, USA.
² U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, USA. yyoshikuni@lbl.gov.

PMID: 30788781
DOI: 10.1007/978-1-4939-9142-6_1

Abstract

Information in public sequence databases on the genomes and metagenomes of microbes and plants has grown rapidly. In conjunction with technological developments in computational identification of biosynthetic gene clusters, molecular biology, synthetic biology, and analytical tools, this has revealed genes for enzymes with optimal and targeted function, as well as a rich pool of uncharacterized metabolic pathways. This chapter discusses different approaches to discovery of genes and metabolic pathways in microbes and plants in nature, such as genomic mining, transcriptome analysis, and metabolite profiling.

Keywords: Computational identification; Enzyme; Gene cluster; Gene library; Gene sequence; Metabolome; Metagenomics; Pathway; Transcriptome.

MeSH terms

Bacteria / genetics
Bacteria / metabolism
Computational Biology / methods*
Databases, Genetic
Fungi / genetics
Fungi / metabolism
Genetic Association Studies* / methods
Genome*
Genomics* / methods
Metabolic Networks and Pathways* / genetics
Molecular Sequence Annotation
Multigene Family
Plants / genetics
Plants / metabolism