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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 aflatrem cluster regions in A. sojae NBRC4239 and A. flavus. Diagram of aflatrem cluster sequence comparison between A. flavus NRRL3357 and A. sojae NBRC4239 strains. (A) ATM1 region. (B) ATM2 region.
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DSR009F7: Comparison of aflatrem cluster regions in A. sojae NBRC4239 and A. flavus. Diagram of aflatrem cluster sequence comparison between A. flavus NRRL3357 and A. sojae NBRC4239 strains. (A) ATM1 region. (B) ATM2 region.

Mentions: The A. sojae genome was analysed for the aflatrem biosynthesis gene cluster found in A. flavus.27 Aflatrem biosynthesis genes in A. flavus are known to consist of genes required to synthesize the intermediate paspaline (atmG, atmC, atmM, and atmB) as well as genes required to convert paspaline to aflatrem (atmP, atmQ, and atmD), which are encoded at two separate loci ATM1 and ATM2 in A. flavus, respectively.27 ATM1 (34 816 bp) and ATM2 (25 256 bp) were analysed for the A. oryzae and A. sojae genomes by BLASTN. We found almost identical sequences to ATM1 and ATM2 with a few base substitutions in A. oryzae. In contrast, five gaps with >100 bp were found in the corresponding region to ATM1 locus in A. sojae (Fig. 7A). In Gap 4, a 1140-bp sequence in A. flavus was replaced by unrelated 6138-bp sequence in A. sojae (Fig. 7A). Nine gaps with >100 bp were also observed in the corresponding region to ATM2 locus in A. sojae (Fig. 7B). In Gap 7, a 2761-bp sequence in A. flavus was replaced by unrelated 11 493-bp sequence in A. sojae (Fig. 7B). All these gaps found in A. sojae were present in the non-coding regions. A frameshift due to single base insertion in exon 7 of atmQ was reported to account for the non-productivity of aflatrem in A. oryzae,27 but such mutation was not found in A. sojae in this study. The presence of insertions in A. sojae NBRC4239 was confirmed by PCR (Supplementary Fig. S4).Figure 7.


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 aflatrem cluster regions in A. sojae NBRC4239 and A. flavus. Diagram of aflatrem cluster sequence comparison between A. flavus NRRL3357 and A. sojae NBRC4239 strains. (A) ATM1 region. (B) ATM2 region.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

DSR009F7: Comparison of aflatrem cluster regions in A. sojae NBRC4239 and A. flavus. Diagram of aflatrem cluster sequence comparison between A. flavus NRRL3357 and A. sojae NBRC4239 strains. (A) ATM1 region. (B) ATM2 region.
Mentions: The A. sojae genome was analysed for the aflatrem biosynthesis gene cluster found in A. flavus.27 Aflatrem biosynthesis genes in A. flavus are known to consist of genes required to synthesize the intermediate paspaline (atmG, atmC, atmM, and atmB) as well as genes required to convert paspaline to aflatrem (atmP, atmQ, and atmD), which are encoded at two separate loci ATM1 and ATM2 in A. flavus, respectively.27 ATM1 (34 816 bp) and ATM2 (25 256 bp) were analysed for the A. oryzae and A. sojae genomes by BLASTN. We found almost identical sequences to ATM1 and ATM2 with a few base substitutions in A. oryzae. In contrast, five gaps with >100 bp were found in the corresponding region to ATM1 locus in A. sojae (Fig. 7A). In Gap 4, a 1140-bp sequence in A. flavus was replaced by unrelated 6138-bp sequence in A. sojae (Fig. 7A). Nine gaps with >100 bp were also observed in the corresponding region to ATM2 locus in A. sojae (Fig. 7B). In Gap 7, a 2761-bp sequence in A. flavus was replaced by unrelated 11 493-bp sequence in A. sojae (Fig. 7B). All these gaps found in A. sojae were present in the non-coding regions. A frameshift due to single base insertion in exon 7 of atmQ was reported to account for the non-productivity of aflatrem in A. oryzae,27 but such mutation was not found in A. sojae in this study. The presence of insertions in A. sojae NBRC4239 was confirmed by PCR (Supplementary Fig. S4).Figure 7.

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