De novo genome assembly and analysis of Zalaria sp. Him3, a novel fructooligosaccharides producing yeast
Abstract Background Zalaria sp. Him3 was reported as a novel fructooligosaccharides (FOS) producing yeast. However, Zalaria spp. have not been widely known and have been erroneously classified as a different black yeast, Aureobasidium pullulans. In this study, de novo genome assembly and analysis of...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-11-01
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| Series: | BMC Genomic Data |
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| Online Access: | https://doi.org/10.1186/s12863-022-01094-2 |
| _version_ | 1797988472691097600 |
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| author | Jun Yoshikawa Minenosuke Matsutani Mayumi Maeda Yutaka Kashiwagi Kenji Maehashi |
| author_facet | Jun Yoshikawa Minenosuke Matsutani Mayumi Maeda Yutaka Kashiwagi Kenji Maehashi |
| author_sort | Jun Yoshikawa |
| collection | DOAJ |
| description | Abstract Background Zalaria sp. Him3 was reported as a novel fructooligosaccharides (FOS) producing yeast. However, Zalaria spp. have not been widely known and have been erroneously classified as a different black yeast, Aureobasidium pullulans. In this study, de novo genome assembly and analysis of Zalaria sp. Him3 was demonstrated to confirm the existence of a potential enzyme that facilitates FOS production and to compare with the genome of A. pullulans. Results The genome of Zalaria sp. Him3 was analyzed; the total read bases and total number of reads were 6.38 Gbp and 42,452,134 reads, respectively. The assembled genome sequence was calculated to be 22.38 Mbp, with 207 contigs, N50 of 885,387, L50 of 10, GC content of 53.8%, and 7,496 genes. g2419, g3120, and g3700 among the predicted genes were annotated as cellulase, xylanase, and β-fructofuranosidase (FFase), respectively. When the read sequences were mapped to A. pullulans EXF-150 genome as a reference, a small amount of reads (3.89%) corresponded to the reference genome. Phylogenetic tree analysis, which was based on the conserved sequence set consisting of 2,362 orthologs in the genome, indicated genetic differences between Zalaria sp. Him3 and Aureobasidium spp. Conclusion The differences between Zalaria and Aureobasidium spp. were evident at the genome level. g3700 identified in the Zalaria sp. Him3 likely does not encode a highly transfructosyl FFase because the motif sequences were unlike those in other FFases involved in FOS production. Therefore, strain Him3 may produce another FFase. Furthermore, several genes with promising functions were identified and might elicit further interest in Zalaria yeast. |
| first_indexed | 2024-04-11T08:03:25Z |
| format | Article |
| id | doaj.art-2edcec0a888f4fdeaabe3ac8812b94a5 |
| institution | Directory Open Access Journal |
| issn | 2730-6844 |
| language | English |
| last_indexed | 2024-04-11T08:03:25Z |
| publishDate | 2022-11-01 |
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| record_format | Article |
| series | BMC Genomic Data |
| spelling | doaj.art-2edcec0a888f4fdeaabe3ac8812b94a52022-12-22T04:35:37ZengBMCBMC Genomic Data2730-68442022-11-012311710.1186/s12863-022-01094-2De novo genome assembly and analysis of Zalaria sp. Him3, a novel fructooligosaccharides producing yeastJun Yoshikawa0Minenosuke Matsutani1Mayumi Maeda2Yutaka Kashiwagi3Kenji Maehashi4Department of Fermentation Science, Faculty of Applied Bioscience, Tokyo University of AgricultureNODAI Genome Research Center, Tokyo University of AgricultureDepartment of Fermentation Science, Faculty of Applied Bioscience, Tokyo University of AgricultureDepartment of Fermentation Science, Faculty of Applied Bioscience, Tokyo University of AgricultureDepartment of Fermentation Science, Faculty of Applied Bioscience, Tokyo University of AgricultureAbstract Background Zalaria sp. Him3 was reported as a novel fructooligosaccharides (FOS) producing yeast. However, Zalaria spp. have not been widely known and have been erroneously classified as a different black yeast, Aureobasidium pullulans. In this study, de novo genome assembly and analysis of Zalaria sp. Him3 was demonstrated to confirm the existence of a potential enzyme that facilitates FOS production and to compare with the genome of A. pullulans. Results The genome of Zalaria sp. Him3 was analyzed; the total read bases and total number of reads were 6.38 Gbp and 42,452,134 reads, respectively. The assembled genome sequence was calculated to be 22.38 Mbp, with 207 contigs, N50 of 885,387, L50 of 10, GC content of 53.8%, and 7,496 genes. g2419, g3120, and g3700 among the predicted genes were annotated as cellulase, xylanase, and β-fructofuranosidase (FFase), respectively. When the read sequences were mapped to A. pullulans EXF-150 genome as a reference, a small amount of reads (3.89%) corresponded to the reference genome. Phylogenetic tree analysis, which was based on the conserved sequence set consisting of 2,362 orthologs in the genome, indicated genetic differences between Zalaria sp. Him3 and Aureobasidium spp. Conclusion The differences between Zalaria and Aureobasidium spp. were evident at the genome level. g3700 identified in the Zalaria sp. Him3 likely does not encode a highly transfructosyl FFase because the motif sequences were unlike those in other FFases involved in FOS production. Therefore, strain Him3 may produce another FFase. Furthermore, several genes with promising functions were identified and might elicit further interest in Zalaria yeast.https://doi.org/10.1186/s12863-022-01094-2ZalariaGenome assemblyBlack yeastβ-fructofuranosidase |
| spellingShingle | Jun Yoshikawa Minenosuke Matsutani Mayumi Maeda Yutaka Kashiwagi Kenji Maehashi De novo genome assembly and analysis of Zalaria sp. Him3, a novel fructooligosaccharides producing yeast BMC Genomic Data Zalaria Genome assembly Black yeast β-fructofuranosidase |
| title | De novo genome assembly and analysis of Zalaria sp. Him3, a novel fructooligosaccharides producing yeast |
| title_full | De novo genome assembly and analysis of Zalaria sp. Him3, a novel fructooligosaccharides producing yeast |
| title_fullStr | De novo genome assembly and analysis of Zalaria sp. Him3, a novel fructooligosaccharides producing yeast |
| title_full_unstemmed | De novo genome assembly and analysis of Zalaria sp. Him3, a novel fructooligosaccharides producing yeast |
| title_short | De novo genome assembly and analysis of Zalaria sp. Him3, a novel fructooligosaccharides producing yeast |
| title_sort | de novo genome assembly and analysis of zalaria sp him3 a novel fructooligosaccharides producing yeast |
| topic | Zalaria Genome assembly Black yeast β-fructofuranosidase |
| url | https://doi.org/10.1186/s12863-022-01094-2 |
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