Unraveling the Polysaccharide Biosynthesis Potential of <i>Ganoderma lucidum</i>: A Chromosome-Level Assembly Using Hi-C Sequencing
<i>Ganoderma lucidum</i> exhibits the ability to synthesize a diverse range of biologically active molecules with significant pharmaceutical potential, including xylomannan and fucogalactan, which have demonstrated antitumor activity. However, there exists considerable intra-species vari...
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MDPI AG
2023-10-01
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| Series: | Journal of Fungi |
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| Online Access: | https://www.mdpi.com/2309-608X/9/10/1020 |
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| author | Ignat V. Sonets Nikita V. Dovidchenko Sergey V. Ulianov Maria S. Yarina Stanislav I. Koshechkin Sergey V. Razin Larissa M. Krasnopolskaya Alexander V. Tyakht |
| author_facet | Ignat V. Sonets Nikita V. Dovidchenko Sergey V. Ulianov Maria S. Yarina Stanislav I. Koshechkin Sergey V. Razin Larissa M. Krasnopolskaya Alexander V. Tyakht |
| author_sort | Ignat V. Sonets |
| collection | DOAJ |
| description | <i>Ganoderma lucidum</i> exhibits the ability to synthesize a diverse range of biologically active molecules with significant pharmaceutical potential, including xylomannan and fucogalactan, which have demonstrated antitumor activity. However, there exists considerable intra-species variability in the capacity to produce these metabolites at high concentrations, likely reflecting the high genomic diversity observed from a limited number of strains sequenced to date. We employed high-throughput shotgun sequencing to obtain the complete genome sequence of <i>G. lucidum</i> strain 5.1, which is distinguished by its remarkable xylomannan synthesis capabilities. Through the utilization of semi-automatic reordering based on conformation capture (Hi-C) data, we substantially enhanced the assembly process, resulting in the generation of 12 chromosome-level scaffolds with a cumulative length of 39 Mbp. By employing both de novo and homology-based approaches, we performed comprehensive annotation of the genome, thereby identifying a diverse repertoire of genes likely involved in polysaccharide biosynthesis. The genome sequence generated in this study serves as a valuable resource for elucidating the molecular mechanisms underlying the medicinal potential of <i>Ganoderma</i> species, discovering novel pharmaceutically valuable compounds, and elucidating the ecological mechanisms of the species. Furthermore, the chromosome contact map obtained for the first time for this species extends our understanding of 3D fungal genomics and provides insights into the functional and structural organization within the fungal kingdom. |
| first_indexed | 2024-03-10T21:08:20Z |
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| id | doaj.art-dd4273eec19b4b2d8b05e8e421a6422e |
| institution | Directory Open Access Journal |
| issn | 2309-608X |
| language | English |
| last_indexed | 2024-03-10T21:08:20Z |
| publishDate | 2023-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Journal of Fungi |
| spelling | doaj.art-dd4273eec19b4b2d8b05e8e421a6422e2023-11-19T17:01:08ZengMDPI AGJournal of Fungi2309-608X2023-10-01910102010.3390/jof9101020Unraveling the Polysaccharide Biosynthesis Potential of <i>Ganoderma lucidum</i>: A Chromosome-Level Assembly Using Hi-C SequencingIgnat V. Sonets0Nikita V. Dovidchenko1Sergey V. Ulianov2Maria S. Yarina3Stanislav I. Koshechkin4Sergey V. Razin5Larissa M. Krasnopolskaya6Alexander V. Tyakht7Institute of Gene Biology, 34/5 Vavilova Street, 119334 Moscow, RussiaKnomics LLC, 34 Bld. 1 Narodnogo Opolcheniya Street, 123423 Moscow, RussiaInstitute of Gene Biology, 34/5 Vavilova Street, 119334 Moscow, RussiaGause Institute of New Antibiotics, 11 B. Pirogovskaya Street, 119021 Moscow, RussiaKnomics LLC, 34 Bld. 1 Narodnogo Opolcheniya Street, 123423 Moscow, RussiaInstitute of Gene Biology, 34/5 Vavilova Street, 119334 Moscow, RussiaGause Institute of New Antibiotics, 11 B. Pirogovskaya Street, 119021 Moscow, RussiaInstitute of Gene Biology, 34/5 Vavilova Street, 119334 Moscow, Russia<i>Ganoderma lucidum</i> exhibits the ability to synthesize a diverse range of biologically active molecules with significant pharmaceutical potential, including xylomannan and fucogalactan, which have demonstrated antitumor activity. However, there exists considerable intra-species variability in the capacity to produce these metabolites at high concentrations, likely reflecting the high genomic diversity observed from a limited number of strains sequenced to date. We employed high-throughput shotgun sequencing to obtain the complete genome sequence of <i>G. lucidum</i> strain 5.1, which is distinguished by its remarkable xylomannan synthesis capabilities. Through the utilization of semi-automatic reordering based on conformation capture (Hi-C) data, we substantially enhanced the assembly process, resulting in the generation of 12 chromosome-level scaffolds with a cumulative length of 39 Mbp. By employing both de novo and homology-based approaches, we performed comprehensive annotation of the genome, thereby identifying a diverse repertoire of genes likely involved in polysaccharide biosynthesis. The genome sequence generated in this study serves as a valuable resource for elucidating the molecular mechanisms underlying the medicinal potential of <i>Ganoderma</i> species, discovering novel pharmaceutically valuable compounds, and elucidating the ecological mechanisms of the species. Furthermore, the chromosome contact map obtained for the first time for this species extends our understanding of 3D fungal genomics and provides insights into the functional and structural organization within the fungal kingdom.https://www.mdpi.com/2309-608X/9/10/1020Hi-C-assisted genome assemblymedicinal mushroomschromosome conformation capturefungal polysaccharides |
| spellingShingle | Ignat V. Sonets Nikita V. Dovidchenko Sergey V. Ulianov Maria S. Yarina Stanislav I. Koshechkin Sergey V. Razin Larissa M. Krasnopolskaya Alexander V. Tyakht Unraveling the Polysaccharide Biosynthesis Potential of <i>Ganoderma lucidum</i>: A Chromosome-Level Assembly Using Hi-C Sequencing Journal of Fungi Hi-C-assisted genome assembly medicinal mushrooms chromosome conformation capture fungal polysaccharides |
| title | Unraveling the Polysaccharide Biosynthesis Potential of <i>Ganoderma lucidum</i>: A Chromosome-Level Assembly Using Hi-C Sequencing |
| title_full | Unraveling the Polysaccharide Biosynthesis Potential of <i>Ganoderma lucidum</i>: A Chromosome-Level Assembly Using Hi-C Sequencing |
| title_fullStr | Unraveling the Polysaccharide Biosynthesis Potential of <i>Ganoderma lucidum</i>: A Chromosome-Level Assembly Using Hi-C Sequencing |
| title_full_unstemmed | Unraveling the Polysaccharide Biosynthesis Potential of <i>Ganoderma lucidum</i>: A Chromosome-Level Assembly Using Hi-C Sequencing |
| title_short | Unraveling the Polysaccharide Biosynthesis Potential of <i>Ganoderma lucidum</i>: A Chromosome-Level Assembly Using Hi-C Sequencing |
| title_sort | unraveling the polysaccharide biosynthesis potential of i ganoderma lucidum i a chromosome level assembly using hi c sequencing |
| topic | Hi-C-assisted genome assembly medicinal mushrooms chromosome conformation capture fungal polysaccharides |
| url | https://www.mdpi.com/2309-608X/9/10/1020 |
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