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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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Phylogenic analysis of serine carboxypeptidase in five Aspergillus species. ORFs of serine carboxypeptidase with Pfam domain scores of >150 were analysed by ClustalW and were drawn by TreeView for five Aspergillus species. Filled circles, A. sojae; filled squares, A. oryzae; filled diamonds, A. flavus; triangle, A. nidulans; inverted triangles, A. fumigatus. Blue lines indicate the genes in common with all five Aspergillus species. Green lines indicate the genes in common with three species in Aspergillus section Flavi. Red shows the gene unique to A. sojae. Oranges show extra homologues in A. oryzae reported in Machida et al.6
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DSR009F1: Phylogenic analysis of serine carboxypeptidase in five Aspergillus species. ORFs of serine carboxypeptidase with Pfam domain scores of >150 were analysed by ClustalW and were drawn by TreeView for five Aspergillus species. Filled circles, A. sojae; filled squares, A. oryzae; filled diamonds, A. flavus; triangle, A. nidulans; inverted triangles, A. fumigatus. Blue lines indicate the genes in common with all five Aspergillus species. Green lines indicate the genes in common with three species in Aspergillus section Flavi. Red shows the gene unique to A. sojae. Oranges show extra homologues in A. oryzae reported in Machida et al.6

Mentions: Phylogenic tree for serine carboxypeptidases based on sequences with domain scores >150 was constructed and then compared for A. sojae NBRC4239, A. oryzae RIB40, A. flavus NRRL3357, A. fumigatus Af293, and A. nidulans FGSC A4 (Fig. 1). We found that A. sojae NBRC4239 possesses a serine carboxypeptidase gene (scaffold00048.369) that has low sequence similarity with the other four species. This gene was also included in the 132 ORFs that had <70% identity against nr (refer to the ‘Comparative genomics’ section). The similarity search of scaffold00048.369 against the ORFs of A. oryzae RIB40 by BLASTP identified a gene AO090103000026 with the closest match of 56% identity. AO090103000026 was annotated as a serine carboxypeptidase in A. oryzae RIB40 (Fig. 1). In addition, Scaffold00048.369 was found to have the highest similarity to carboxypeptidase S1 in Neosartorya fischeri NRRL181 with 58% identity by searching against the nr NCBI database by BLASTP. From these results, scaffold00048.369 is likely to be a serine carboxypeptidase unique to A. sojae NBRC4239. We confirmed the expression of scaffold00048.369 by RT–PCR for mRNA isolated from A. sojae NBRC4239 incubated in wheat bran media. The sequencing of the RT–PCR product revealed a sequence identical to the predicted ORF, indicating that our ORF prediction for scaffold00048.36 was correct, and this gene is expressed in wheat bran media (data not shown).Figure 1.


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)

Phylogenic analysis of serine carboxypeptidase in five Aspergillus species. ORFs of serine carboxypeptidase with Pfam domain scores of >150 were analysed by ClustalW and were drawn by TreeView for five Aspergillus species. Filled circles, A. sojae; filled squares, A. oryzae; filled diamonds, A. flavus; triangle, A. nidulans; inverted triangles, A. fumigatus. Blue lines indicate the genes in common with all five Aspergillus species. Green lines indicate the genes in common with three species in Aspergillus section Flavi. Red shows the gene unique to A. sojae. Oranges show extra homologues in A. oryzae reported in Machida et al.6
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

DSR009F1: Phylogenic analysis of serine carboxypeptidase in five Aspergillus species. ORFs of serine carboxypeptidase with Pfam domain scores of >150 were analysed by ClustalW and were drawn by TreeView for five Aspergillus species. Filled circles, A. sojae; filled squares, A. oryzae; filled diamonds, A. flavus; triangle, A. nidulans; inverted triangles, A. fumigatus. Blue lines indicate the genes in common with all five Aspergillus species. Green lines indicate the genes in common with three species in Aspergillus section Flavi. Red shows the gene unique to A. sojae. Oranges show extra homologues in A. oryzae reported in Machida et al.6
Mentions: Phylogenic tree for serine carboxypeptidases based on sequences with domain scores >150 was constructed and then compared for A. sojae NBRC4239, A. oryzae RIB40, A. flavus NRRL3357, A. fumigatus Af293, and A. nidulans FGSC A4 (Fig. 1). We found that A. sojae NBRC4239 possesses a serine carboxypeptidase gene (scaffold00048.369) that has low sequence similarity with the other four species. This gene was also included in the 132 ORFs that had <70% identity against nr (refer to the ‘Comparative genomics’ section). The similarity search of scaffold00048.369 against the ORFs of A. oryzae RIB40 by BLASTP identified a gene AO090103000026 with the closest match of 56% identity. AO090103000026 was annotated as a serine carboxypeptidase in A. oryzae RIB40 (Fig. 1). In addition, Scaffold00048.369 was found to have the highest similarity to carboxypeptidase S1 in Neosartorya fischeri NRRL181 with 58% identity by searching against the nr NCBI database by BLASTP. From these results, scaffold00048.369 is likely to be a serine carboxypeptidase unique to A. sojae NBRC4239. We confirmed the expression of scaffold00048.369 by RT–PCR for mRNA isolated from A. sojae NBRC4239 incubated in wheat bran media. The sequencing of the RT–PCR product revealed a sequence identical to the predicted ORF, indicating that our ORF prediction for scaffold00048.36 was correct, and this gene is expressed in wheat bran media (data not shown).Figure 1.

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