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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 A. oryzae predicted secondary metabolite clusters with A. sojae. Secondary metabolite Clusters 38 (A) and 47 (B) which were predicted from A. oryzae RIB40 by SMURF were compared with sequences in A. sojaeNBRC4239 by Harr plots.
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DSR009F5: Comparison of A. oryzae predicted secondary metabolite clusters with A. sojae. Secondary metabolite Clusters 38 (A) and 47 (B) which were predicted from A. oryzae RIB40 by SMURF were compared with sequences in A. sojaeNBRC4239 by Harr plots.

Mentions: The 56 secondary metabolite cluster sequences were predicted using SMURF in the A. oryzae RIB40 genome.25 We analysed these clusters for the A. sojae NBRC4239 genome by Harr plots. Out of the 56 predicted secondary metabolite clusters, 24 clusters were found to be almost identical and the remaining 32 clusters differed from those in A. oryzae RIB40 (Supplementary Table S5). Aspergillus sojae NBRC4239 had no sequence homologous to Cluster 51 located on the end of chromosome 5 in A. oryzae. In addition, large portions of Clusters 38 (non-ribosomal peptide synthetase: NRPS) and 47 (NRPS) were missing in A. sojae NBRC4239 (Fig. 5). For Cluster 38, A. sojae NBRC4239 had a replaced 363-bp sequence and a sequence containing the 5′ portion of 460 bp and the 3′ portion of 2.9 kb generated by a deletion of 23 188 bp from the 26 571 bp (SC026: 1081838–1108408) predicted in A. oryzae RIB40 (Fig. 5A). For Cluster 47, the 3′ portion of 14 kb in 30 338 bp (SC102: 1249352–1279689) predicted in A. oryzae RIB40 was replaced by unrelated 17-kb sequence (Fig. 5B). Also, small deletions and insertions were observed in the remaining 29 clusters (data not shown).Figure 5.


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 A. oryzae predicted secondary metabolite clusters with A. sojae. Secondary metabolite Clusters 38 (A) and 47 (B) which were predicted from A. oryzae RIB40 by SMURF were compared with sequences in A. sojaeNBRC4239 by Harr plots.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

DSR009F5: Comparison of A. oryzae predicted secondary metabolite clusters with A. sojae. Secondary metabolite Clusters 38 (A) and 47 (B) which were predicted from A. oryzae RIB40 by SMURF were compared with sequences in A. sojaeNBRC4239 by Harr plots.
Mentions: The 56 secondary metabolite cluster sequences were predicted using SMURF in the A. oryzae RIB40 genome.25 We analysed these clusters for the A. sojae NBRC4239 genome by Harr plots. Out of the 56 predicted secondary metabolite clusters, 24 clusters were found to be almost identical and the remaining 32 clusters differed from those in A. oryzae RIB40 (Supplementary Table S5). Aspergillus sojae NBRC4239 had no sequence homologous to Cluster 51 located on the end of chromosome 5 in A. oryzae. In addition, large portions of Clusters 38 (non-ribosomal peptide synthetase: NRPS) and 47 (NRPS) were missing in A. sojae NBRC4239 (Fig. 5). For Cluster 38, A. sojae NBRC4239 had a replaced 363-bp sequence and a sequence containing the 5′ portion of 460 bp and the 3′ portion of 2.9 kb generated by a deletion of 23 188 bp from the 26 571 bp (SC026: 1081838–1108408) predicted in A. oryzae RIB40 (Fig. 5A). For Cluster 47, the 3′ portion of 14 kb in 30 338 bp (SC102: 1249352–1279689) predicted in A. oryzae RIB40 was replaced by unrelated 17-kb sequence (Fig. 5B). Also, small deletions and insertions were observed in the remaining 29 clusters (data not shown).Figure 5.

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