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Comparative genome analysis between Aspergillus oryzae strains reveals close relationship between sites of mutation localization and regions of highly divergent genes among Aspergillus species.

Umemura M, Koike H, Yamane N, Koyama Y, Satou Y, Kikuzato I, Teruya M, Tsukahara M, Imada Y, Wachi Y, Miwa Y, Yano S, Tamano K, Kawarabayasi Y, Fujimori KE, Machida M, Hirano T - DNA Res. (2012)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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

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.

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Related in: MedlinePlus

Organizations of SBs and NSBs in the A. oryzae, A. fumigatus, and A. nidulans genomes. SBs, which were identified from syntenic analysis between A. oryzae, A. fumigatus, and A. nidulans,1 are common between the genomes, whereas NSBs in A. oryzae consist of the extra genetic regions from other two smaller genome sequences.
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DSS019F1: Organizations of SBs and NSBs in the A. oryzae, A. fumigatus, and A. nidulans genomes. SBs, which were identified from syntenic analysis between A. oryzae, A. fumigatus, and A. nidulans,1 are common between the genomes, whereas NSBs in A. oryzae consist of the extra genetic regions from other two smaller genome sequences.

Mentions: As a wild-type strain of A. oryzae, the genome sequence of A. oryzae RIB40 [37 Mb; the National Research Institute of Brewing (NRIB), Japan; NITE Biological Resource Center (NBRC) stock no. 100959; American Type Culture Collection (ATCC) no. 42149] was completed1 and compared with those of Aspergillus nidulans (30 Mb)2 and Aspergillus fumigatus (29 Mb),3 revealing that the A. oryzae genome could be characterized into distinct syntenic blocks (SBs) and non-SBs (NSBs). Because the three species are phylogenetically closely related, SBs occupy ∼70–80% of the three genomes.2 NSBs are considered to be unique genetic elements of individual species, and the A. oryzae genome has the largest total size of NSBs (Fig. 1).Figure 1.


Comparative genome analysis between Aspergillus oryzae strains reveals close relationship between sites of mutation localization and regions of highly divergent genes among Aspergillus species.

Umemura M, Koike H, Yamane N, Koyama Y, Satou Y, Kikuzato I, Teruya M, Tsukahara M, Imada Y, Wachi Y, Miwa Y, Yano S, Tamano K, Kawarabayasi Y, Fujimori KE, Machida M, Hirano T - DNA Res. (2012)

Organizations of SBs and NSBs in the A. oryzae, A. fumigatus, and A. nidulans genomes. SBs, which were identified from syntenic analysis between A. oryzae, A. fumigatus, and A. nidulans,1 are common between the genomes, whereas NSBs in A. oryzae consist of the extra genetic regions from other two smaller genome sequences.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3473370&req=5

DSS019F1: Organizations of SBs and NSBs in the A. oryzae, A. fumigatus, and A. nidulans genomes. SBs, which were identified from syntenic analysis between A. oryzae, A. fumigatus, and A. nidulans,1 are common between the genomes, whereas NSBs in A. oryzae consist of the extra genetic regions from other two smaller genome sequences.
Mentions: As a wild-type strain of A. oryzae, the genome sequence of A. oryzae RIB40 [37 Mb; the National Research Institute of Brewing (NRIB), Japan; NITE Biological Resource Center (NBRC) stock no. 100959; American Type Culture Collection (ATCC) no. 42149] was completed1 and compared with those of Aspergillus nidulans (30 Mb)2 and Aspergillus fumigatus (29 Mb),3 revealing that the A. oryzae genome could be characterized into distinct syntenic blocks (SBs) and non-SBs (NSBs). Because the three species are phylogenetically closely related, SBs occupy ∼70–80% of the three genomes.2 NSBs are considered to be unique genetic elements of individual species, and the A. oryzae genome has the largest total size of NSBs (Fig. 1).Figure 1.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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

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.

Show MeSH
Related in: MedlinePlus