Genomic platform for efficient identification of fungal secondary metabolism genes

Myco Umemura, Hideaki Koike, Jin Kawano, Tomoko Ishii, Yuki Miyamura, Tsutomu Ikegami, Goro Terai, Toshitaka Kumagai, Itaru Takeda, Koichi Tamano, Katsuhisa Horimoto, Jiujiang Yu, Kiyoshi Asai, Masayuki Machida

Author address: 

Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 17-2-1 Higashi-Nijo, Tsukisamu, Sapporo, Hokkaido 062-8517, Japan


Fungal secondary metabolites (SMs) are structurally diverse natural compounds, which are thought to have a great potential not only for medical industry but also for chemical and environmental industries. Since the expansion of sequencing microbial genomes in the 19908223;s, it has been known that SM genes are far more plentiful in microbial genomes than was expected before sequencing. For most of the genes, we have no information about the conditions for their expression, thus, probably 90% or more of them have remained unexamined. In order to accelerate analysis and utilization of the unaddressed useful genes, we have developed a platform comprised of NGS (next-generation sequencer), LC/MS and bioinformatics tools specialized for high throughput analysis of multiple fungal genomes. By using the platform, twelve novel fungal genomes can be sequenced within about two weeks by SOLiD 5500 XL. Our in-house pipelines allow quick and accurate analysis of genome, gene modeling, transcriptome and successive prediction of SM gene clusters. Once a compound of interest is detected by any methods including biological, chemical or physical methods, the corresponding SM gene cluster can be rapidly predicted, typically within a month. We have successfully determined gene clusters of kojic acid, ustiloxin B and other previously unknown compounds to date. A remarkable feature of our platform is the ability to detect SM gene clusters without a so-called SM core gene such as PKS, NRPS and terpene, which allows the scientific community to expand our target SM gene clusters far beyond those already examined.

abstract No: 


Full conference title: 

Asian Mycological Congress 2013 and the 13th International Marine and Freshwater Mycology Symposium
    • AMC 2013