Comparative Genome Analysis Between Aspergillus oryzae Strains Reveals Close Relationship Between Sites of Mutation Localization and Regions of Highly Divergent Genes among Aspergillus Species

Abstract

Aspergillus oryzae has been utilized for over 1000 years in Japan for the production of various traditional foods, and a large number of A. oryzae strains have been isolated and/or selected for the effective fermentation of food ingredients. Characteristics of genetic alterations among the strains used are of particular interest in studies of A. oryzae. Here, we have sequenced the whole genome of an industrial fungal isolate, A. oryzae RIB326, by using a next-generation sequencing system and compared the data with those of A. oryzae RIB40, a wild-type strain sequenced in 2005. The aim of this study was to evaluate the mutation pressure on the non-syntenic blocks (NSBs) of the genome, which were previously identified through comparative genomic analysis of A. oryzae, Aspergillus fumigatus, and Aspergillus nidulans. We found that genes within the NSBs of RIB326 accumulate mutations more frequently than those within the SBs, regardless of their distance from the telomeres or of their expression level. Our findings suggest that the high mutation frequency of NSBs might contribute to maintaining the diversity of the A. oryzae genome.

Genomic and transcriptomic comparison of Aspergillus oryzae strains: a case study in soy sauce koji fermentation

“…Besides the well-known amylolytic enzymes that are highly expressed in soy sauce-producing strains [22, 28, 43], various cellulolytic, xylanolytic and pectinolytic enzymes were also expressed in significantly higher levels in RD2 in the ME and ES stages (Fig. 4a).…”

High sequence variations in the region containing genes encoding a cellular morphogenesis protein and the repressor of sexual development help to reveal origins of Aspergillus oryzae

“…Group III strains account for only about 4% of the NRIB collection. A genome sequence comparison between RIB326 of group III and RIB40 indicates extensive deletions (3.3%) in the genome of the former (Umemura et al, 2012). Nonetheless, both have the samA-rosA/RIB40 type.…”

“…The module of CLC Genomic Workbench (http://www.slsbio.com) -CLCbio N NGS Core Tools N Map Reads to Reference was used. BLAST search and manual sequence analysis on assembled genome sequences (contigs) of A. oryzae RIB326 (Umemura et al, 2012) and strain 3.042, a soy-sauce producing strain used in China (Zhao et al, 2013), were also performed to identify these genetic traits.…”

“…The genome of A. flavus NRRL3357, an L strain, also is about 37 Mb and contains 13,485 genes (Payne et al, 2006). Genome sequences of seven additional strains of A. flavus and A. oryzae though not yet well assembled are available (Gibbons et al, 2012;Umemura et al, 2012). A comparison of genomes of A. oryzae RIB40 and A. oryzae 3.042 indicates they are mostly collinear but with several translocations (Zhao et al, 2013).…”

MIDDAS-M: Motif-Independent De Novo Detection of Secondary Metabolite Gene Clusters through the Integration of Genome Sequencing and Transcriptome Data

“…NSBs harbor genes that have roles in the transport and metabolism of various compounds [13] and are highly divergent between species [16]–[18]. Two-thirds of the genes in NSBs are not homologous with any genes with known functions [13].…”