Unraveling the Polysaccharide Biosynthesis Potential of Ganoderma lucidum: A Chromosome-Level Assembly Using Hi-C Sequencing

doi:10.3390/jof9101020

. 2023 Oct 16;9(10):1020.

doi: 10.3390/jof9101020.

Unraveling the Polysaccharide Biosynthesis Potential of Ganoderma lucidum: A Chromosome-Level Assembly Using Hi-C Sequencing

Ignat V Sonets¹, Nikita V Dovidchenko^{2

3}, Sergey V Ulianov^{1

4}, Maria S Yarina⁵, Stanislav I Koshechkin², Sergey V Razin^{1

4}, Larissa M Krasnopolskaya⁵, Alexander V Tyakht^{1

2

6}

Affiliations

¹ Institute of Gene Biology, 34/5 Vavilova Street, 119334 Moscow, Russia.
² Knomics LLC, 34 Bld. 1 Narodnogo Opolcheniya Street, 123423 Moscow, Russia.
³ Institute of Protein Research, 4 Institutskaya Street, 142290 Pushchino, Russia.
⁴ Faculty of Biology, Lomonosov Moscow State University, GSP-1, Leninskie Gory, 119991 Moscow, Russia.
⁵ Gause Institute of New Antibiotics, 11 B. Pirogovskaya Street, 119021 Moscow, Russia.
⁶ Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, 34/5 Vavilova Street, 119334 Moscow, Russia.

PMID: 37888276
PMCID: PMC10608111
DOI: 10.3390/jof9101020

Unraveling the Polysaccharide Biosynthesis Potential of Ganoderma lucidum: A Chromosome-Level Assembly Using Hi-C Sequencing

Ignat V Sonets et al. J Fungi (Basel). 2023.

. 2023 Oct 16;9(10):1020.

doi: 10.3390/jof9101020.

Authors

Ignat V Sonets¹, Nikita V Dovidchenko^{2

3}, Sergey V Ulianov^{1

4}, Maria S Yarina⁵, Stanislav I Koshechkin², Sergey V Razin^{1

4}, Larissa M Krasnopolskaya⁵, Alexander V Tyakht^{1

2

6}

Affiliations

¹ Institute of Gene Biology, 34/5 Vavilova Street, 119334 Moscow, Russia.
² Knomics LLC, 34 Bld. 1 Narodnogo Opolcheniya Street, 123423 Moscow, Russia.
³ Institute of Protein Research, 4 Institutskaya Street, 142290 Pushchino, Russia.
⁴ Faculty of Biology, Lomonosov Moscow State University, GSP-1, Leninskie Gory, 119991 Moscow, Russia.
⁵ Gause Institute of New Antibiotics, 11 B. Pirogovskaya Street, 119021 Moscow, Russia.
⁶ Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, 34/5 Vavilova Street, 119334 Moscow, Russia.

PMID: 37888276
PMCID: PMC10608111
DOI: 10.3390/jof9101020

Abstract

Ganoderma lucidum 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 G. lucidum 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 Ganoderma 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.

Keywords: Hi-C-assisted genome assembly; chromosome conformation capture; fungal polysaccharides; medicinal mushrooms.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

**Figure 1**
Gene annotation workflows. (A) Homology-based. (B) De novo.

**Figure 2**
Chromosome contact intensity map of the *G. lucidum* genome following the reordering of scaffolds. Resolution: 100 kbp. Super-scaffolds/quasi-chromosomes derived from Hi-C data are depicted in blue, while the largest scaffolds from the original WGS assembly are illustrated in green.

**Figure 3**
Clavaric acid biosynthesis gene cluster according to the antiSMASH prediction.

See this image and copyright information in PMC

References

1. He M.-Q., Zhao R.-L., Liu D.-M., Denchev T.T., Begerow D., Yurkov A., Kemler M., Millanes A.M., Wedin M., McTaggart A.R., et al. Species diversity of Basidiomycota. Fungal Divers. 2022;114:281–325. doi: 10.1007/s13225-021-00497-3. - DOI
1. Gressler M., Löhr N.A., Schäfer T., Lawrinowitz S., Seibold P.S., Hoffmeister D. Mind the mushroom: Natural product biosynthetic genes and enzymes of Basidiomycota. Nat. Prod. Rep. 2021;38:702–722. doi: 10.1039/D0NP00077A. - DOI - PubMed
1. Sharma C., Bhardwaj N., Sharma A., Tuli H.S., Batra P., Beniwal V., Gupta G.K., Sharma A.K. Bioactive metabolites of Ganoderma lucidum: Factors, mechanism and broad spectrum therapeutic potential. J. Herb. Med. 2019;17–18:100268. doi: 10.1016/j.hermed.2019.100268. - DOI
1. Lu J., He R., Sun P., Zhang F., Linhardt R.J., Zhang A. Molecular mechanisms of bioactive polysaccharides from Ganoderma lucidum (Lingzhi), a review. Int. J. Biol. Macromol. 2020;150:765–774. doi: 10.1016/j.ijbiomac.2020.02.035. - DOI - PubMed
1. Ahmad F., Ahmad F.A., Khan M.I., Alsayegh A.A., Wahab S., Alam M.I., Ahmed F. Ganoderma lucidum: A potential source to surmount viral infections through β-glucans immunomodulatory and triterpenoids antiviral properties. Int. J. Biol. Macromol. 2021;187:769–779. doi: 10.1016/j.ijbiomac.2021.06.122. - DOI - PubMed

Grants and funding

LinkOut - more resources

Full Text Sources
Miscellaneous
- NCI CPTAC Assay Portal

[1] He M.-Q., Zhao R.-L., Liu D.-M., Denchev T.T., Begerow D., Yurkov A., Kemler M., Millanes A.M., Wedin M., McTaggart A.R., et al. Species diversity of Basidiomycota. Fungal Divers. 2022;114:281–325. doi: 10.1007/s13225-021-00497-3. - DOI

[2] He M.-Q., Zhao R.-L., Liu D.-M., Denchev T.T., Begerow D., Yurkov A., Kemler M., Millanes A.M., Wedin M., McTaggart A.R., et al. Species diversity of Basidiomycota. Fungal Divers. 2022;114:281–325. doi: 10.1007/s13225-021-00497-3. - DOI

[3] Gressler M., Löhr N.A., Schäfer T., Lawrinowitz S., Seibold P.S., Hoffmeister D. Mind the mushroom: Natural product biosynthetic genes and enzymes of Basidiomycota. Nat. Prod. Rep. 2021;38:702–722. doi: 10.1039/D0NP00077A. - DOI - PubMed

[4] Gressler M., Löhr N.A., Schäfer T., Lawrinowitz S., Seibold P.S., Hoffmeister D. Mind the mushroom: Natural product biosynthetic genes and enzymes of Basidiomycota. Nat. Prod. Rep. 2021;38:702–722. doi: 10.1039/D0NP00077A. - DOI - PubMed

[5] Sharma C., Bhardwaj N., Sharma A., Tuli H.S., Batra P., Beniwal V., Gupta G.K., Sharma A.K. Bioactive metabolites of Ganoderma lucidum: Factors, mechanism and broad spectrum therapeutic potential. J. Herb. Med. 2019;17–18:100268. doi: 10.1016/j.hermed.2019.100268. - DOI

[6] Sharma C., Bhardwaj N., Sharma A., Tuli H.S., Batra P., Beniwal V., Gupta G.K., Sharma A.K. Bioactive metabolites of Ganoderma lucidum: Factors, mechanism and broad spectrum therapeutic potential. J. Herb. Med. 2019;17–18:100268. doi: 10.1016/j.hermed.2019.100268. - DOI

[7] Lu J., He R., Sun P., Zhang F., Linhardt R.J., Zhang A. Molecular mechanisms of bioactive polysaccharides from Ganoderma lucidum (Lingzhi), a review. Int. J. Biol. Macromol. 2020;150:765–774. doi: 10.1016/j.ijbiomac.2020.02.035. - DOI - PubMed

[8] Lu J., He R., Sun P., Zhang F., Linhardt R.J., Zhang A. Molecular mechanisms of bioactive polysaccharides from Ganoderma lucidum (Lingzhi), a review. Int. J. Biol. Macromol. 2020;150:765–774. doi: 10.1016/j.ijbiomac.2020.02.035. - DOI - PubMed

[9] Ahmad F., Ahmad F.A., Khan M.I., Alsayegh A.A., Wahab S., Alam M.I., Ahmed F. Ganoderma lucidum: A potential source to surmount viral infections through β-glucans immunomodulatory and triterpenoids antiviral properties. Int. J. Biol. Macromol. 2021;187:769–779. doi: 10.1016/j.ijbiomac.2021.06.122. - DOI - PubMed

[10] Ahmad F., Ahmad F.A., Khan M.I., Alsayegh A.A., Wahab S., Alam M.I., Ahmed F. Ganoderma lucidum: A potential source to surmount viral infections through β-glucans immunomodulatory and triterpenoids antiviral properties. Int. J. Biol. Macromol. 2021;187:769–779. doi: 10.1016/j.ijbiomac.2021.06.122. - DOI - PubMed

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

Unraveling the Polysaccharide Biosynthesis Potential of Ganoderma lucidum: A Chromosome-Level Assembly Using Hi-C Sequencing

Affiliations

Unraveling the Polysaccharide Biosynthesis Potential of Ganoderma lucidum: A Chromosome-Level Assembly Using Hi-C Sequencing

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

Similar articles

References

Grants and funding

LinkOut - more resources

Full Text Sources

Miscellaneous