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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

Mutation of SB and NSB genes based on KOG functional categories. (a) Gene numbers and (b) averaged amino acid substitution frequencies within SBs and NSBs are plotted for each KOG. The gray and white bars indicate the values for SBs and NSBs, respectively. Each KOG category was classified into three meta-categories: I, information storage and processing (J to B); II, cellular process and signalling (D to W); and III, metabolism (C to Q), as described in the Materials and methods section. In (b), the values for categories that did not include ≤10 genes were not drawn to avoid misinterpretation of biological insignificance.
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DSS019F6: Mutation of SB and NSB genes based on KOG functional categories. (a) Gene numbers and (b) averaged amino acid substitution frequencies within SBs and NSBs are plotted for each KOG. The gray and white bars indicate the values for SBs and NSBs, respectively. Each KOG category was classified into three meta-categories: I, information storage and processing (J to B); II, cellular process and signalling (D to W); and III, metabolism (C to Q), as described in the Materials and methods section. In (b), the values for categories that did not include ≤10 genes were not drawn to avoid misinterpretation of biological insignificance.

Mentions: Figure 6 depicts the gene numbers and mean amino acid substitution frequencies of SB and NSB genes for the major functional categories of the KOG of proteins.16 The number of NSB genes belonging to meta-category I, which represents information storage and processing, was significantly smaller than that of SB genes (Fig. 6a). The number of NSB genes belonging to meta-category III, which includes secondary metabolism genes (Q), hydrolases, and transporters, was significantly greater than the other two meta-categories (Fig. 6a). This result is in accordance with our previous finding that NSBs are the regions where secretory hydrolases and secondary metabolic genes unique to A. oryzae.5 In addition, it was determined that the amino acid substitution frequency was higher within NSBs for all examined functional categories (Fig. 6b).Figure 6.


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)

Mutation of SB and NSB genes based on KOG functional categories. (a) Gene numbers and (b) averaged amino acid substitution frequencies within SBs and NSBs are plotted for each KOG. The gray and white bars indicate the values for SBs and NSBs, respectively. Each KOG category was classified into three meta-categories: I, information storage and processing (J to B); II, cellular process and signalling (D to W); and III, metabolism (C to Q), as described in the Materials and methods section. In (b), the values for categories that did not include ≤10 genes were not drawn to avoid misinterpretation of biological insignificance.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

DSS019F6: Mutation of SB and NSB genes based on KOG functional categories. (a) Gene numbers and (b) averaged amino acid substitution frequencies within SBs and NSBs are plotted for each KOG. The gray and white bars indicate the values for SBs and NSBs, respectively. Each KOG category was classified into three meta-categories: I, information storage and processing (J to B); II, cellular process and signalling (D to W); and III, metabolism (C to Q), as described in the Materials and methods section. In (b), the values for categories that did not include ≤10 genes were not drawn to avoid misinterpretation of biological insignificance.
Mentions: Figure 6 depicts the gene numbers and mean amino acid substitution frequencies of SB and NSB genes for the major functional categories of the KOG of proteins.16 The number of NSB genes belonging to meta-category I, which represents information storage and processing, was significantly smaller than that of SB genes (Fig. 6a). The number of NSB genes belonging to meta-category III, which includes secondary metabolism genes (Q), hydrolases, and transporters, was significantly greater than the other two meta-categories (Fig. 6a). This result is in accordance with our previous finding that NSBs are the regions where secretory hydrolases and secondary metabolic genes unique to A. oryzae.5 In addition, it was determined that the amino acid substitution frequency was higher within NSBs for all examined functional categories (Fig. 6b).Figure 6.

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