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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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Mutation of SB and NSB genes in relation to the distance from chromosomal termini. The percentages of (a) genes with mutation and (b) averaged amino acid substitutions are shown for all SB and NSB genes located in the genome, and those located greater than 100- or 500-kb distant from the closest chromosomal termini.
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DSS019F3: Mutation of SB and NSB genes in relation to the distance from chromosomal termini. The percentages of (a) genes with mutation and (b) averaged amino acid substitutions are shown for all SB and NSB genes located in the genome, and those located greater than 100- or 500-kb distant from the closest chromosomal termini.

Mentions: Figure 3 shows the frequency of gene alterations for CDS located within SBs and NSBs according to their location within the RIB326 genome. The analysis revealed that genes containing mutations were ∼10% more frequent within NSBs than those located in SBs and were more prevalent when excluding genes closest (100 or 500 kb) from chromosomal termini (Fig. 3a). Similarly, the amino acid substitution ratio of all NSB genes was higher than that observed in SB genes and further increased on the exclusion of genes located closest to termini (Fig. 3b). These results indicate that NSBs accumulate a greater number of mutations than SBs regardless of the chromosomal location.Figure 3.


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 in relation to the distance from chromosomal termini. The percentages of (a) genes with mutation and (b) averaged amino acid substitutions are shown for all SB and NSB genes located in the genome, and those located greater than 100- or 500-kb distant from the closest chromosomal termini.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

DSS019F3: Mutation of SB and NSB genes in relation to the distance from chromosomal termini. The percentages of (a) genes with mutation and (b) averaged amino acid substitutions are shown for all SB and NSB genes located in the genome, and those located greater than 100- or 500-kb distant from the closest chromosomal termini.
Mentions: Figure 3 shows the frequency of gene alterations for CDS located within SBs and NSBs according to their location within the RIB326 genome. The analysis revealed that genes containing mutations were ∼10% more frequent within NSBs than those located in SBs and were more prevalent when excluding genes closest (100 or 500 kb) from chromosomal termini (Fig. 3a). Similarly, the amino acid substitution ratio of all NSB genes was higher than that observed in SB genes and further increased on the exclusion of genes located closest to termini (Fig. 3b). These results indicate that NSBs accumulate a greater number of mutations than SBs regardless of the chromosomal location.Figure 3.

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