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Draft genome sequencing and comparative analysis of Aspergillus sojae NBRC4239.

Sato A, Oshima K, Noguchi H, Ogawa M, Takahashi T, Oguma T, Koyama Y, Itoh T, Hattori M, Hanya Y - DNA Res. (2011)

Bottom Line: Of the 2847 open reading frames with Pfam domain scores of >150 found in A. sojae NBRC4239, 81.7% had a high degree of similarity with the genes of A. oryzae.Comparison of 56 gene clusters for secondary metabolites between A. sojae NBRC4239 and A. oryzae revealed that 24 clusters were conserved, whereas 32 clusters differed between them that included a deletion of 18 508 bp containing mfs1, mao1, dmaT, and pks-nrps for the cyclopiazonic acid (CPA) biosynthesis, explaining the no productivity of CPA in A. sojae.The A. sojae NBRC4239 genome data will be useful to characterize functional features of the koji moulds used in Japanese industries.

View Article: PubMed Central - PubMed

Affiliation: Research and Development Division, Kikkoman Corporation, 399 Noda, Noda City, Chiba 278-0037, Japan.

ABSTRACT
We conducted genome sequencing of the filamentous fungus Aspergillus sojae NBRC4239 isolated from the koji used to prepare Japanese soy sauce. We used the 454 pyrosequencing technology and investigated the genome with respect to enzymes and secondary metabolites in comparison with other Aspergilli sequenced. Assembly of 454 reads generated a non-redundant sequence of 39.5-Mb possessing 13 033 putative genes and 65 scaffolds composed of 557 contigs. Of the 2847 open reading frames with Pfam domain scores of >150 found in A. sojae NBRC4239, 81.7% had a high degree of similarity with the genes of A. oryzae. Comparative analysis identified serine carboxypeptidase and aspartic protease genes unique to A. sojae NBRC4239. While A. oryzae possessed three copies of α-amyalse gene, A. sojae NBRC4239 possessed only a single copy. Comparison of 56 gene clusters for secondary metabolites between A. sojae NBRC4239 and A. oryzae revealed that 24 clusters were conserved, whereas 32 clusters differed between them that included a deletion of 18 508 bp containing mfs1, mao1, dmaT, and pks-nrps for the cyclopiazonic acid (CPA) biosynthesis, explaining the no productivity of CPA in A. sojae. The A. sojae NBRC4239 genome data will be useful to characterize functional features of the koji moulds used in Japanese industries.

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Comparison of α-amylase genes and their flanking regions. Map of α-amylase and flanking regions. Grey box, conserved regions; shaded box, regions unique to A. sojae; white box, regions unique to A. oryzae ; black box, inversed regions; black arrow, α-amylase gene ORF; black triangle, PCR primer-binding site.
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DSR009F3: Comparison of α-amylase genes and their flanking regions. Map of α-amylase and flanking regions. Grey box, conserved regions; shaded box, regions unique to A. sojae; white box, regions unique to A. oryzae ; black box, inversed regions; black arrow, α-amylase gene ORF; black triangle, PCR primer-binding site.

Mentions: The above-mentioned three α-amylase genes and their flanking 20-kb regions of A. oryzae were further compared with the corresponding regions in A. sojae NBRC4239 scaffolds. We investigated whether the difference in α-amylase gene copy numbers results from the difference in genomic structures. The results are shown in Fig. 3. In the A. sojae amy1 region, the 12.5-kb sequence including 2.2 kb of amy1 ORF, and its promoter and terminator regions were absent. Instead of the 12.5-kb region, a unique 2.9-kb sequence excluding amy1 was present. This was also the case for amy2, where the 12.4-kb region including amy2 ORF, and its promoter and terminator regions were absent, but a sequence unique as observed in the amy1 region was not present in amy2. Furthermore, a 7.2-kb region was also absent and an inverted region was observed near the missing amy2 regions in A. sojae. These results indicated that this region of the A. sojae genome was structurally rearranged. In the amy3 region, we found that amy3 structural genes and its terminator regions were conserved between A. oryzae and A. sojae. However, a 1.9-kb insertion sequence was found at 0.53 kb upstream of the translation initiation site in the A. oryzae amy3 promoter.Figure 3.


Draft genome sequencing and comparative analysis of Aspergillus sojae NBRC4239.

Sato A, Oshima K, Noguchi H, Ogawa M, Takahashi T, Oguma T, Koyama Y, Itoh T, Hattori M, Hanya Y - DNA Res. (2011)

Comparison of α-amylase genes and their flanking regions. Map of α-amylase and flanking regions. Grey box, conserved regions; shaded box, regions unique to A. sojae; white box, regions unique to A. oryzae ; black box, inversed regions; black arrow, α-amylase gene ORF; black triangle, PCR primer-binding site.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3111232&req=5

DSR009F3: Comparison of α-amylase genes and their flanking regions. Map of α-amylase and flanking regions. Grey box, conserved regions; shaded box, regions unique to A. sojae; white box, regions unique to A. oryzae ; black box, inversed regions; black arrow, α-amylase gene ORF; black triangle, PCR primer-binding site.
Mentions: The above-mentioned three α-amylase genes and their flanking 20-kb regions of A. oryzae were further compared with the corresponding regions in A. sojae NBRC4239 scaffolds. We investigated whether the difference in α-amylase gene copy numbers results from the difference in genomic structures. The results are shown in Fig. 3. In the A. sojae amy1 region, the 12.5-kb sequence including 2.2 kb of amy1 ORF, and its promoter and terminator regions were absent. Instead of the 12.5-kb region, a unique 2.9-kb sequence excluding amy1 was present. This was also the case for amy2, where the 12.4-kb region including amy2 ORF, and its promoter and terminator regions were absent, but a sequence unique as observed in the amy1 region was not present in amy2. Furthermore, a 7.2-kb region was also absent and an inverted region was observed near the missing amy2 regions in A. sojae. These results indicated that this region of the A. sojae genome was structurally rearranged. In the amy3 region, we found that amy3 structural genes and its terminator regions were conserved between A. oryzae and A. sojae. However, a 1.9-kb insertion sequence was found at 0.53 kb upstream of the translation initiation site in the A. oryzae amy3 promoter.Figure 3.

Bottom Line: Of the 2847 open reading frames with Pfam domain scores of >150 found in A. sojae NBRC4239, 81.7% had a high degree of similarity with the genes of A. oryzae.Comparison of 56 gene clusters for secondary metabolites between A. sojae NBRC4239 and A. oryzae revealed that 24 clusters were conserved, whereas 32 clusters differed between them that included a deletion of 18 508 bp containing mfs1, mao1, dmaT, and pks-nrps for the cyclopiazonic acid (CPA) biosynthesis, explaining the no productivity of CPA in A. sojae.The A. sojae NBRC4239 genome data will be useful to characterize functional features of the koji moulds used in Japanese industries.

View Article: PubMed Central - PubMed

Affiliation: Research and Development Division, Kikkoman Corporation, 399 Noda, Noda City, Chiba 278-0037, Japan.

ABSTRACT
We conducted genome sequencing of the filamentous fungus Aspergillus sojae NBRC4239 isolated from the koji used to prepare Japanese soy sauce. We used the 454 pyrosequencing technology and investigated the genome with respect to enzymes and secondary metabolites in comparison with other Aspergilli sequenced. Assembly of 454 reads generated a non-redundant sequence of 39.5-Mb possessing 13 033 putative genes and 65 scaffolds composed of 557 contigs. Of the 2847 open reading frames with Pfam domain scores of >150 found in A. sojae NBRC4239, 81.7% had a high degree of similarity with the genes of A. oryzae. Comparative analysis identified serine carboxypeptidase and aspartic protease genes unique to A. sojae NBRC4239. While A. oryzae possessed three copies of α-amyalse gene, A. sojae NBRC4239 possessed only a single copy. Comparison of 56 gene clusters for secondary metabolites between A. sojae NBRC4239 and A. oryzae revealed that 24 clusters were conserved, whereas 32 clusters differed between them that included a deletion of 18 508 bp containing mfs1, mao1, dmaT, and pks-nrps for the cyclopiazonic acid (CPA) biosynthesis, explaining the no productivity of CPA in A. sojae. The A. sojae NBRC4239 genome data will be useful to characterize functional features of the koji moulds used in Japanese industries.

Show MeSH
Related in: MedlinePlus