Long-read sequencing reveals absence of 5mC in Ogataea parapolymorpha DL-1 genome and introduces telomere-to-telomere assembly
BackgroundOgataea parapolymorpha DL-1 is a versatile thermotolerant organism with numerous applications in biotechnology, particularly in the production of recombinant proteins and the study of methanol metabolism and peroxisome functions. This study presents a comprehensive genome and methylome ana...
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Frontiers Media S.A.
2025-05-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2025.1574332/full |
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| author | Andrey Eremin Alexander Sergeev Alexander Sergeev Arthur Kopylov Arthur Kopylov Vladimir Rodin Daniil Malyshev Tatiana Panova Igor Polyakov Maria Zvereva |
| author_facet | Andrey Eremin Alexander Sergeev Alexander Sergeev Arthur Kopylov Arthur Kopylov Vladimir Rodin Daniil Malyshev Tatiana Panova Igor Polyakov Maria Zvereva |
| author_sort | Andrey Eremin |
| collection | DOAJ |
| description | BackgroundOgataea parapolymorpha DL-1 is a versatile thermotolerant organism with numerous applications in biotechnology, particularly in the production of recombinant proteins and the study of methanol metabolism and peroxisome functions. This study presents a comprehensive genome and methylome analysis of Ogataea parapolymorpha DL-1 using long-read sequencing technology. The research builds upon previous short-read sequencing efforts, revealing enhancements in genome assembly and epigenomic insights.MethodsWe used long-read sequencing technology to achieve a telomere-to-telomere (T2T) genome assembly of Ogataea parapolymorpha DL-1. High-quality reads were obtained and assembled de novo, followed by polishing to enhance accuracy. The genome was analyzed to identify coding genes, telomeric motifs, rRNA genes, and methylation patterns, including the detection of 5mC and 6 mA modifications. Epigenetic features were further assessed and validated through liquid chromatography-mass spectrometry.ResultsKey findings include the absence of 5 mC DNA modification and the presence of 6 mA in the genome, unusual telomere regulation mechanism based on the addition of non-telomeric dT and the introduction of long-read enhanced telomere-to-telomere assembly.ConclusionThis work provides deeper insights into the yeast’s genome organization and methylation patterns, contributing to the understanding of its genetics and therefore potential biotechnological applications. |
| format | Article |
| id | doaj-art-b363d5f987e546fdbfccebefcef8fdce |
| institution | OA Journals |
| issn | 1664-8021 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj-art-b363d5f987e546fdbfccebefcef8fdce2025-08-20T02:28:19ZengFrontiers Media S.A.Frontiers in Genetics1664-80212025-05-011610.3389/fgene.2025.15743321574332Long-read sequencing reveals absence of 5mC in Ogataea parapolymorpha DL-1 genome and introduces telomere-to-telomere assemblyAndrey Eremin0Alexander Sergeev1Alexander Sergeev2Arthur Kopylov3Arthur Kopylov4Vladimir Rodin5Daniil Malyshev6Tatiana Panova7Igor Polyakov8Maria Zvereva9Lomonosov Moscow State University, Moscow, RussiaLomonosov Moscow State University, Moscow, RussiaInstitute of Biomedical Chemistry, Moscow, RussiaLomonosov Moscow State University, Moscow, RussiaInstitute of Biomedical Chemistry, Moscow, RussiaLomonosov Moscow State University, Moscow, RussiaLomonosov Moscow State University, Moscow, RussiaLomonosov Moscow State University, Moscow, RussiaLomonosov Moscow State University, Moscow, RussiaLomonosov Moscow State University, Moscow, RussiaBackgroundOgataea parapolymorpha DL-1 is a versatile thermotolerant organism with numerous applications in biotechnology, particularly in the production of recombinant proteins and the study of methanol metabolism and peroxisome functions. This study presents a comprehensive genome and methylome analysis of Ogataea parapolymorpha DL-1 using long-read sequencing technology. The research builds upon previous short-read sequencing efforts, revealing enhancements in genome assembly and epigenomic insights.MethodsWe used long-read sequencing technology to achieve a telomere-to-telomere (T2T) genome assembly of Ogataea parapolymorpha DL-1. High-quality reads were obtained and assembled de novo, followed by polishing to enhance accuracy. The genome was analyzed to identify coding genes, telomeric motifs, rRNA genes, and methylation patterns, including the detection of 5mC and 6 mA modifications. Epigenetic features were further assessed and validated through liquid chromatography-mass spectrometry.ResultsKey findings include the absence of 5 mC DNA modification and the presence of 6 mA in the genome, unusual telomere regulation mechanism based on the addition of non-telomeric dT and the introduction of long-read enhanced telomere-to-telomere assembly.ConclusionThis work provides deeper insights into the yeast’s genome organization and methylation patterns, contributing to the understanding of its genetics and therefore potential biotechnological applications.https://www.frontiersin.org/articles/10.3389/fgene.2025.1574332/fullgenomicslong-read sequencingmethylomicsOgataea parapolymorpha DL-1T2T-assembly |
| spellingShingle | Andrey Eremin Alexander Sergeev Alexander Sergeev Arthur Kopylov Arthur Kopylov Vladimir Rodin Daniil Malyshev Tatiana Panova Igor Polyakov Maria Zvereva Long-read sequencing reveals absence of 5mC in Ogataea parapolymorpha DL-1 genome and introduces telomere-to-telomere assembly Frontiers in Genetics genomics long-read sequencing methylomics Ogataea parapolymorpha DL-1 T2T-assembly |
| title | Long-read sequencing reveals absence of 5mC in Ogataea parapolymorpha DL-1 genome and introduces telomere-to-telomere assembly |
| title_full | Long-read sequencing reveals absence of 5mC in Ogataea parapolymorpha DL-1 genome and introduces telomere-to-telomere assembly |
| title_fullStr | Long-read sequencing reveals absence of 5mC in Ogataea parapolymorpha DL-1 genome and introduces telomere-to-telomere assembly |
| title_full_unstemmed | Long-read sequencing reveals absence of 5mC in Ogataea parapolymorpha DL-1 genome and introduces telomere-to-telomere assembly |
| title_short | Long-read sequencing reveals absence of 5mC in Ogataea parapolymorpha DL-1 genome and introduces telomere-to-telomere assembly |
| title_sort | long read sequencing reveals absence of 5mc in ogataea parapolymorpha dl 1 genome and introduces telomere to telomere assembly |
| topic | genomics long-read sequencing methylomics Ogataea parapolymorpha DL-1 T2T-assembly |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2025.1574332/full |
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