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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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Distribution of mutations in the RIB326 genome. (a) The nucleotide substitution percentage and (b) amino acid conservation ratio in the A. oryzae RIB40 genome against RIB326 were plotted using a 10-kb window with a 5-kb overlap. Each chromosomal region (I–VIII) is indicated by dark green stepwise line located at the bottom of the graph, and the position of the centromere in each chromosome deduced from the terminal of scaffolds is indicated by red arrows. The short vertical gray lines located in at the middle of the figure represent the position of NSBs determined from syntenic analysis between A. oryzae, A. nidulans, and A. fumigatus.1
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DSS019F2: Distribution of mutations in the RIB326 genome. (a) The nucleotide substitution percentage and (b) amino acid conservation ratio in the A. oryzae RIB40 genome against RIB326 were plotted using a 10-kb window with a 5-kb overlap. Each chromosomal region (I–VIII) is indicated by dark green stepwise line located at the bottom of the graph, and the position of the centromere in each chromosome deduced from the terminal of scaffolds is indicated by red arrows. The short vertical gray lines located in at the middle of the figure represent the position of NSBs determined from syntenic analysis between A. oryzae, A. nidulans, and A. fumigatus.1

Mentions: To grasp genetic alterations between the two A. oryzae strains, the localization of nucleotide alterations and amino acid substitutions between RIB326 and RIB40 were mapped on the RIB40 genome (Fig. 2). In regions proximal to centromeres, a decrease in the nucleotide substitution frequency was observed, indicating that these regions are subjected to strong selective pressure. In contrast, the nucleotide substitution ratio was higher in regions proximal to chromosomal termini (sub-telomeric regions). This result is in good agreement with the fact that the sub-telomeric regions of yeast and humans are unstable due to telomere loss and thus, accumulate mutations at a higher rate.17–19 In Caenorhabditis elegans, the single-nucleotide polymorphism density on the chromosomal terminus was ∼4.5-fold more abundant than that found on the central part of the chromosome.20 The location of mutations appears to be correlated with NSBs, which are generally localized proximal to chromosomal termini. Pairwise comparison of the genes between the two genomes showed that only 1.2% of RIB326 genes had more than 20% deletions/substitutions of amino acids from corresponding RIB40 genes. Therefore, almost all SBs and NSBs in RIB326 are located at the same positions of those in RIB40 and the higher mutation frequency in NSBs is consistent using either RIB326 or RIB40 genomes.Figure 2.


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)

Distribution of mutations in the RIB326 genome. (a) The nucleotide substitution percentage and (b) amino acid conservation ratio in the A. oryzae RIB40 genome against RIB326 were plotted using a 10-kb window with a 5-kb overlap. Each chromosomal region (I–VIII) is indicated by dark green stepwise line located at the bottom of the graph, and the position of the centromere in each chromosome deduced from the terminal of scaffolds is indicated by red arrows. The short vertical gray lines located in at the middle of the figure represent the position of NSBs determined from syntenic analysis between A. oryzae, A. nidulans, and A. fumigatus.1
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

DSS019F2: Distribution of mutations in the RIB326 genome. (a) The nucleotide substitution percentage and (b) amino acid conservation ratio in the A. oryzae RIB40 genome against RIB326 were plotted using a 10-kb window with a 5-kb overlap. Each chromosomal region (I–VIII) is indicated by dark green stepwise line located at the bottom of the graph, and the position of the centromere in each chromosome deduced from the terminal of scaffolds is indicated by red arrows. The short vertical gray lines located in at the middle of the figure represent the position of NSBs determined from syntenic analysis between A. oryzae, A. nidulans, and A. fumigatus.1
Mentions: To grasp genetic alterations between the two A. oryzae strains, the localization of nucleotide alterations and amino acid substitutions between RIB326 and RIB40 were mapped on the RIB40 genome (Fig. 2). In regions proximal to centromeres, a decrease in the nucleotide substitution frequency was observed, indicating that these regions are subjected to strong selective pressure. In contrast, the nucleotide substitution ratio was higher in regions proximal to chromosomal termini (sub-telomeric regions). This result is in good agreement with the fact that the sub-telomeric regions of yeast and humans are unstable due to telomere loss and thus, accumulate mutations at a higher rate.17–19 In Caenorhabditis elegans, the single-nucleotide polymorphism density on the chromosomal terminus was ∼4.5-fold more abundant than that found on the central part of the chromosome.20 The location of mutations appears to be correlated with NSBs, which are generally localized proximal to chromosomal termini. Pairwise comparison of the genes between the two genomes showed that only 1.2% of RIB326 genes had more than 20% deletions/substitutions of amino acids from corresponding RIB40 genes. Therefore, almost all SBs and NSBs in RIB326 are located at the same positions of those in RIB40 and the higher mutation frequency in NSBs is consistent using either RIB326 or RIB40 genomes.Figure 2.

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