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Open Access Research article

Genome sequence and transcriptome analyses of the thermophilic zygomycete fungus Rhizomucor miehei

Peng Zhou1, Guoqiang Zhang2, Shangwu Chen1, Zhengqiang Jiang1*, Yanbin Tang1, Bernard Henrissat34, Qiaojuan Yan5, Shaoqing Yang1, Chin-Fu Chen6, Bing Zhang2* and Zhenglin Du2

Author Affiliations

1 Department of Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China

2 Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China

3 UMR 7257 - Centre National de la Recherche Scientifique & Aix-Marseille Université, Marseille 13288, France

4 Department of Biological Sciences, King Abdulazziz University, Jeddah, Saudi Arabia

5 Bioresource Utilization Laboratory, College of Engineering, China Agricultural University, Beijing 100083, China

6 Office of Bioinformatics and Center for Molecular Studies, 113 Gregor Mendel Circle Greenwood, SC 29646, USA

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BMC Genomics 2014, 15:294  doi:10.1186/1471-2164-15-294

Published: 21 April 2014

Abstract

Background

The zygomycete fungi like Rhizomucor miehei have been extensively exploited for the production of various enzymes. As a thermophilic fungus, R. miehei is capable of growing at temperatures that approach the upper limits for all eukaryotes. To date, over hundreds of fungal genomes are publicly available. However, Zygomycetes have been rarely investigated both genetically and genomically.

Results

Here, we report the genome of R. miehei CAU432 to explore the thermostable enzymatic repertoire of this fungus. The assembled genome size is 27.6-million-base (Mb) with 10,345 predicted protein-coding genes. Even being thermophilic, the G + C contents of fungal whole genome (43.8%) and coding genes (47.4%) are less than 50%. Phylogenetically, R. miehei is more closerly related to Phycomyces blakesleeanus than to Mucor circinelloides and Rhizopus oryzae. The genome of R. miehei harbors a large number of genes encoding secreted proteases, which is consistent with the characteristics of R. miehei being a rich producer of proteases. The transcriptome profile of R. miehei showed that the genes responsible for degrading starch, glucan, protein and lipid were highly expressed.

Conclusions

The genome information of R. miehei will facilitate future studies to better understand the mechanisms of fungal thermophilic adaptation and the exploring of the potential of R. miehei in industrial-scale production of thermostable enzymes. Based on the existence of a large repertoire of amylolytic, proteolytic and lipolytic genes in the genome, R. miehei has potential in the production of a variety of such enzymes.

Keywords:
Rhizomucor miehei; Genome; Transcriptome; Thermophilic fungus; Thermostable enzymes