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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

Distribution of deletions, insertions, and inversions in the RIB40 genome. The regions of deletion (red), insertion (green), and inversion (blue) were evaluated between the RIB40 reference scaffolds and RIB326 scaffolds obtained from de novo assembly. Each RIB40 chromosome is indicated in a step graph at the bottom of the chart. For insertions, the starting points were plotted.
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DSS019F4: Distribution of deletions, insertions, and inversions in the RIB40 genome. The regions of deletion (red), insertion (green), and inversion (blue) were evaluated between the RIB40 reference scaffolds and RIB326 scaffolds obtained from de novo assembly. Each RIB40 chromosome is indicated in a step graph at the bottom of the chart. For insertions, the starting points were plotted.

Mentions: The distribution of deletions, insertions, and inversions within the RIB326 genome, as mapped on the RIB40 genome, was also determined, revealing that genetic rearrangements also accumulated in NSBs of strain RIB326 (Fig. 4). Table 1 summarizes the number and ratio of deletions, insertions, and inversions in the RIB40 genome sequence against that of RIB326, which were determined using the longest 200 scaffolds (>576 bp) obtained by sequencing of the mate-paired library of RIB326. Notably, 24.2 and 19.8% of the deletions and inversions, respectively, were found within NSBs on the RIB40 genome. Considering that the nucleotides defined as NSBs occupy only 12.4% of the entire genome sequence of RIB40, the results indicate that deletions and inversions are highly enriched in NSBs of A. oryzae.Table 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)

Distribution of deletions, insertions, and inversions in the RIB40 genome. The regions of deletion (red), insertion (green), and inversion (blue) were evaluated between the RIB40 reference scaffolds and RIB326 scaffolds obtained from de novo assembly. Each RIB40 chromosome is indicated in a step graph at the bottom of the chart. For insertions, the starting points were plotted.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

DSS019F4: Distribution of deletions, insertions, and inversions in the RIB40 genome. The regions of deletion (red), insertion (green), and inversion (blue) were evaluated between the RIB40 reference scaffolds and RIB326 scaffolds obtained from de novo assembly. Each RIB40 chromosome is indicated in a step graph at the bottom of the chart. For insertions, the starting points were plotted.
Mentions: The distribution of deletions, insertions, and inversions within the RIB326 genome, as mapped on the RIB40 genome, was also determined, revealing that genetic rearrangements also accumulated in NSBs of strain RIB326 (Fig. 4). Table 1 summarizes the number and ratio of deletions, insertions, and inversions in the RIB40 genome sequence against that of RIB326, which were determined using the longest 200 scaffolds (>576 bp) obtained by sequencing of the mate-paired library of RIB326. Notably, 24.2 and 19.8% of the deletions and inversions, respectively, were found within NSBs on the RIB40 genome. Considering that the nucleotides defined as NSBs occupy only 12.4% of the entire genome sequence of RIB40, the results indicate that deletions and inversions are highly enriched in NSBs of A. oryzae.Table 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