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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

Gene number and averaged amino acid substitution ratios within SBs and NSBs of strain RIB326 against gene expression levels. (a) Gene numbers and (b) averaged amino acid substitution frequencies within SBs and NSBs are plotted against the level of EST. The P-values for the difference between the amino acid substitution ratios within SBs and NSBs were evaluated using the Wilcoxon signed-rank test for each EST level that included greater than four genes. Asterisks indicate a P-value of <0.05 in the graph of NSBs.
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DSS019F5: Gene number and averaged amino acid substitution ratios within SBs and NSBs of strain RIB326 against gene expression levels. (a) Gene numbers and (b) averaged amino acid substitution frequencies within SBs and NSBs are plotted against the level of EST. The P-values for the difference between the amino acid substitution ratios within SBs and NSBs were evaluated using the Wilcoxon signed-rank test for each EST level that included greater than four genes. Asterisks indicate a P-value of <0.05 in the graph of NSBs.

Mentions: Figure 5 shows the number of genes and frequency of amino acid substitutions for genes located within SBs and NSBs against the redundancy of ESTs, which were previously obtained from eight different cultural conditions.15 Our analysis revealed that the percentage of genes within SBs and NSBs decreased as the EST level increased, with the number of NSB genes decreasing at a higher rate than that of SB genes (Fig. 5a). This result is in good agreement with the finding that NSB genes typically have markedly lower expression levels than those of SB genes.4 Nevertheless, a small percentage of NSB genes was detected at EST levels of >10, indicating that several genes within NSBs are functional. As shown in Figure 5b, the average amino acid substitution ratios were significantly (P< 0.05) higher for NSB genes than those of SB genes at any EST level, when greater than four genes were available for the analysis. This result demonstrates that the genes within NSBs accumulated more mutations than those within SBs, even those that exhibited high-expression levels.Figure 5.


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)

Gene number and averaged amino acid substitution ratios within SBs and NSBs of strain RIB326 against gene expression levels. (a) Gene numbers and (b) averaged amino acid substitution frequencies within SBs and NSBs are plotted against the level of EST. The P-values for the difference between the amino acid substitution ratios within SBs and NSBs were evaluated using the Wilcoxon signed-rank test for each EST level that included greater than four genes. Asterisks indicate a P-value of <0.05 in the graph of NSBs.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

DSS019F5: Gene number and averaged amino acid substitution ratios within SBs and NSBs of strain RIB326 against gene expression levels. (a) Gene numbers and (b) averaged amino acid substitution frequencies within SBs and NSBs are plotted against the level of EST. The P-values for the difference between the amino acid substitution ratios within SBs and NSBs were evaluated using the Wilcoxon signed-rank test for each EST level that included greater than four genes. Asterisks indicate a P-value of <0.05 in the graph of NSBs.
Mentions: Figure 5 shows the number of genes and frequency of amino acid substitutions for genes located within SBs and NSBs against the redundancy of ESTs, which were previously obtained from eight different cultural conditions.15 Our analysis revealed that the percentage of genes within SBs and NSBs decreased as the EST level increased, with the number of NSB genes decreasing at a higher rate than that of SB genes (Fig. 5a). This result is in good agreement with the finding that NSB genes typically have markedly lower expression levels than those of SB genes.4 Nevertheless, a small percentage of NSB genes was detected at EST levels of >10, indicating that several genes within NSBs are functional. As shown in Figure 5b, the average amino acid substitution ratios were significantly (P< 0.05) higher for NSB genes than those of SB genes at any EST level, when greater than four genes were available for the analysis. This result demonstrates that the genes within NSBs accumulated more mutations than those within SBs, even those that exhibited high-expression levels.Figure 5.

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