Skip to main content
SpringerLink
Log in

Genome Resequencing and Transcriptome Analysis Reveal the Genetic Diversity of Wolfiporia cocos Germplasm and Genes Related to High Yield

  • Published:
Current Microbiology Aims and scope Submit manuscript

Abstract

Wolfiporia cocos is a saprophytic fungus belonging to the phylum Basidiomycota. The dried sclerotium of this organism has been widely used in traditional Chinese medicine for several thousand years and it is prescribed in many formulations. The W. cocos germplasm resources are complex and diverse, and the molecular mechanisms underlying the growth and development of its sclerotia are unclear. In this study, we used genome resequencing and transcriptome analysis to evaluate the genetic diversity of W. cocos germplasm resources in China and the mechanism of sclerotium growth and development. Phylogenetic and population structure analyses revealed that all the 39 tested strains were divided into three major groups. Most of the strains were clustered into one group, and the remaining strains were clustered into the other two groups. There may be a shared origin of cultivated W. cocos in the main production areas. Transcriptome analysis and quantitative reverse transcription-polymerase chain reaction confirmed that candidate genes related to the yield of W. cocos were mainly enriched in oxidation–reduction and carbohydrate metabolism and highly expressed in the ShenChuan strain, which had the highest comprehensive cultivation score. The findings will be helpful for further understanding the evolution and population structure of W. cocos and determining the functional genes that contribute to the high yield of sclerotia.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

Data Availability

The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, PRJNA762230, PRJNA761862.

References

  1. Hattori T, Hayashi K, Nagao T, Furuta K, Ito M, Suzuki Y (1992) Studies on antinephritic effects of plant components (3): effect of pachyman, a main component of Poria cocos Wolf on original-type anti-GBM nephritis in rats and its mechanisms. Jpn J Pharmacol 59:89–96. https://doi.org/10.1254/jjp.59.89

    Article  CAS  PubMed  Google Scholar 

  2. Wang LY, Wan HJ, Chen LX, Zhang HM, Yu ZY (1993) Studies on chemical constituents from solvent extracts of Poria cocos (Schw.) Wolf. Zhongguo Zhong Yao Za Zhi 18:613–639

    CAS  PubMed  Google Scholar 

  3. Kaminaga T, Yasukawa K, Kanno H, Tai T, Nunoura Y, Takido M (1996) Inhibitory effects of lanostane-type triterpene acids, the components of Poria cocos, on tumor promotion by 12-O-tetradecanoylphorbol-13-acetate in two-stage carcinogenesis in mouse skin. Oncology 53:382–385. https://doi.org/10.1159/000227592

    Article  CAS  PubMed  Google Scholar 

  4. Liu XF, Wang XQ, Xu XF, Zhang XW (2019) Purification, antitumor and anti-inflammation activities of an alkali-soluble and carboxymethyl polysaccharide CMP33 from Poria cocos. Int J Biol Macromol 127:39–47. https://doi.org/10.1016/j.ijbiomac.2019.01.029

    Article  CAS  PubMed  Google Scholar 

  5. Shi CY, Ma QH, Ren MY, Liang DD, Yu QT, Luo JB (2017) Antitumorpharmacological mechanism of the oral liquid of Poriacocos polysaccharide. J Ethnopharmacol 209:24–31. https://doi.org/10.1016/j.jep.2017.07.003

    Article  CAS  PubMed  Google Scholar 

  6. Wang NN, Zhang Y, Wang XP, Huang XW, Fei Y, Yu Y, Shou D (2016) Antioxidant property of water-soluble polysaccharides from Poria cocos Wolf using different extraction methods. Int J Biol Macromol 83:103–110. https://doi.org/10.1016/j.ijbiomac.2015.11.032

    Article  CAS  PubMed  Google Scholar 

  7. Baosong C, Sixian W, Gaoqiang L, Li B, Ying H, Ruilin Z, Hongwei L (2020) Anti-inflammatory diterpenes and steroids from peels of the cultivated edible mushroom Wolfiporia cocos. Phytochem Lett 36:11–16. https://doi.org/10.1016/j.phytol.2020.01.005

    Article  CAS  Google Scholar 

  8. Feng YL, Cao G, Chen DQ, Vaziri ND, Chen L, Zhang J, Wang M, Guo Y, Zhao YY (2019) Microbiome-metabolomics reveals gut microbiota associated with glycine-conjugated metabolites and polyamine metabolism in chronic kidney disease. Cell Mol Life Sci 76:4961–4978. https://doi.org/10.1007/s00018-019-03155-9

    Article  CAS  PubMed  Google Scholar 

  9. Esteban CI (2009) Medicinal interest of Poria cocos (= Wolfiporia extensa). Rev Iberoam Micol 26:103–107. https://doi.org/10.1016/S1130-1406(09)70019-1

    Article  PubMed  Google Scholar 

  10. Li L, Wang KQ, Bai J et al (2008) Study on the revulsive cultivation modes of W. cocos. Mod Chin Med 28:16–17. https://doi.org/10.3969/j.issn.1673-4890.2008.12.004

    Article  Google Scholar 

  11. Li L, Wang KQ, Bian YB, Su W, Wang LY (2011) Technical regulations for the production of Hubei W. cocos strains. Mod Chin Med 11:28–32. https://doi.org/10.3969/j.issn.1673-4890.2011.11.007

    Article  CAS  Google Scholar 

  12. Xu ZY, Meng H, Xiong H, Bian YB (2014) Biological characteristics of teleomorph and optimized in vitro fruiting conditions of the Hoelen medicinal mushroom, Wolfiporia extensa (Higher Basidiomycetes). Int J Med Mushrooms 16:421–429. https://doi.org/10.1615/intjmedmushrooms.v16.i5.20

    Article  PubMed  Google Scholar 

  13. Cheng L, Hou J, Wang W, Ding C, Wang Q, Dai J (2015) Investigation and analysis on the production technology of W. cocos in China. Mod Chin Med 3:195–199. https://doi.org/10.13313/j.issn.1673-4890.2015.3.002

    Article  Google Scholar 

  14. Qu Z, Tao G, Zhu GS, Zhu Y, Liu YX, Liu ZY (2008) RAPD analysis of germplasm resources of Wolfiporia cocos. J Fungal Res 6:170–174

    CAS  Google Scholar 

  15. Cai DF, Chen MY, Guo ZJ et al (2009) Studies on the biological characteristics of Wolfiporia cocos strain. Edible Fungi China 28:23–26. https://doi.org/10.3969/j.issn.1003-8310.2009.01.009

    Article  Google Scholar 

  16. Luo HM, Qian J, Xu ZC et al (2020) The Wolfiporia cocos genome and transcriptome shed light on the formation of its edible and medicinal Sclerotium. Genom Proteom Bioinform 18:455–467. https://doi.org/10.1016/j.gpb.2019.01.007

    Article  Google Scholar 

  17. Hu BX (2017) De novo assembly and transcriptome analysis of mycelium formed sclerotial and sclerotial development in Wolfiporia cocos. Dissertation. Wuhan Polytechnic University. CNKI:CDMD:2.1018.067545

  18. Cai DF (2013) Selection of fine strain of Wolfiporia cocos for pine stump cultivation. Edible Fungi China 32:14–16

    Google Scholar 

  19. Xu TT, Shen BX, Hu K, Jin CS (2013) Identification and preparation of Anhui Poria cocos spaw. Strait Pharm J 10:18–20. https://doi.org/10.3969/j.issn.1006-3765.2013.10.07t

    Article  Google Scholar 

  20. Wang XX, Wang DQ (2011) Problems and countermeasures of Poria cocos in Jinzhai County of Anhui Province. J Anhui Univ Chin Med 30:60–63. https://doi.org/10.3969/j.issn.1000-2219.2011.03.023

    Article  Google Scholar 

  21. Wang KQ, Yin XR, Huang H, Feng HG, Wang Q, Sun G (2012) Production status and industrialization development countermeasures of Poria in Hubei Province. Mod Chin Med 14:24–27. https://doi.org/10.3969/j.issn.1673-4890.2012.12.007

    Article  CAS  Google Scholar 

  22. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics 25:1754–1760. https://doi.org/10.1093/bioinformatics/btp324

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303. https://doi.org/10.1101/gr.107524.110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19:1655–1664. https://doi.org/10.1101/gr.094052.109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Laurentin H, Karlovsky P (2007) AFLP fingerprinting of sesame (Sesamum indicum L.) cultivars: identification, genetic relationship and comparison of AFLP informativeness parameters. Genet Resour Crop Evol 54:1437–1446. https://doi.org/10.1007/s10722-006-9128-y

    Article  Google Scholar 

  27. Qu RZ, Hou L, Lü HL, Li HY (2004) The gene flow of population genetic structure. Yi Chuan 26:377–382. https://doi.org/10.3321/j.issn:0253-9772.2004.03.022

    Article  CAS  PubMed  Google Scholar 

  28. Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12:357–360. https://doi.org/10.1038/nmeth.3317

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Mortazavi A, Williams BA, Mccue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628. https://doi.org/10.1038/nmeth10.1038/nmeth.1226

    Article  CAS  PubMed  Google Scholar 

  30. Tang WR (2013) Preliminary study on the effects of “bait” on yield and quality of the new Sclerotium in Wolfporia cocos. Dissertation. Huazhong Agricultural University. https://doi.org/10.7666/d.Y2394986

  31. Floudas D, Binder M, Riley R et al (2012) The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336:1715–1719. https://doi.org/10.1126/science.1221748

    Article  CAS  PubMed  Google Scholar 

  32. Lu B, Yan J (2003) Sampling strategy for genetic diversity. Biodivers Sci 11:155–161. https://doi.org/10.17520/biods.2003021

    Article  Google Scholar 

  33. Wu SL, Tang SJ, Jin LS, Chen X, Yang YH, Yue L (2018) Quality evaluation and genetic relation identification for different Poria cocos strains. J South Agric 49:8–13

    Google Scholar 

  34. Song Z, Yin Y, Lin Y, Du F, Ren G, Wang Z (2018) The bZIP transcriptional factor activator protein-1 regulates Metarhizium rileyi morphology and mediates microsclerotia formation. Appl Microbiol Biotechnol 102:4577–4588. https://doi.org/10.1007/s00253-018-8941-5

    Article  CAS  PubMed  Google Scholar 

  35. Li B, Tian X, Wang C, Zeng X, Xing Y, Ling H, Yin W, Tian L, Meng Z, Zhang J, Guo S (2017) SWATH label-free proteomics analyses revealed the roles of oxidative stress and antioxidant defensing system in sclerotia formation of Polyporus umbellatus. Sci Rep 7:41283. https://doi.org/10.1038/srep41283

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Georgiou CD (1997) Lipid peroxidation in Sclerotium rolfsii: a new look into the mechanism of sclerotial biogenesis in fungi. Mycol Res 101:460–464. https://doi.org/10.1017/S0953756296002882

    Article  CAS  Google Scholar 

  37. Liu MM, Xing YM, Zhang DW, Guo SX (2015) Transcriptome analysis of genes involved in defence response in Polyporus umbellatus with Armillaria mellea infection. Sci Rep 5:16075. https://doi.org/10.1038/srep16075

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Song C, Liu M, Xing Y, Guo S (2014) ESTs analysis of putative genes engaged in Polyporus umbellatus sclerotial development. Int J Mol Sci 15:15951–15962. https://doi.org/10.3390/ijms150915951

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Choi KD, Kwon JK, Shim JO, Lee SS, Lee T, Lee MW (2002) Sclerotial development of Grifola umbellata. Mycobiology 30:65–69. https://doi.org/10.4489/MYCO.2002.30.2.065

    Article  Google Scholar 

  40. Erental A, Dickman MB, Yarden O (2008) Sclerotial development in Sclerotinia sclerotiorum: awakening molecular analysis of a “Dormant” structure. Fungal Biol Rev 22:6–16. https://doi.org/10.1016/j.fbr.2007.10.001

    Article  Google Scholar 

  41. Georgiou CD, Tairis N, Sotiropoulou A (2000) Hydroxyl radical scavengers inhibit lateral-type sclerotial differentiation and growth in phytopathogenic fungi. Mycologia 92:825–834. https://doi.org/10.1080/00275514.2000.12061226

    Article  CAS  Google Scholar 

  42. Georgiou CD, Zervoudakis G, Tairis N, Kornaros M (2001) β-carotene production and its role in sclerotial differentiation of Sclerotium rolfsii. Fungal Genet Biol 34:11–20. https://doi.org/10.1006/fgbi.2001.1285

    Article  CAS  PubMed  Google Scholar 

  43. Grabherr MG, Haas BJ, Yassour ML et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652. https://doi.org/10.1038/nbt.1883

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Feng YL, Lei P, Tian T (2019) Diuretic activity of some fractions of the epidermis of Poria cocos. Ethnopharmacol 150:1114–1118. https://doi.org/10.1016/j.jep.2013.10.043

    Article  Google Scholar 

  45. King BC, Waxman KD, Nenni NV, Walker LP, Bergstrom GC, Gibson DM (2011) Arsenal of plant cell wall degrading enzymes reflects host preference among plant pathogenic fungi. Biotechnol Biofuels 4:4. https://doi.org/10.1186/1754-6834-4-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Kobira S, Atsumi T, Kakiuchi N, Mikage M (2012) Difference in cultivation characteristics and genetic polymorphism between Chinese and Japanese strains of Wolfiporia cocos Ryvarden et Gilbertson (Poria cocos Wolf). J Nat Med 66:493–499. https://doi.org/10.1007/s11418-011-0612-0

    Article  CAS  PubMed  Google Scholar 

  47. Gan P, Ikeda K, Irieda H, Narusaka M, O’Connell RJ, Narusaka Y, Takano Y, Kubo Y, Shirasu K (2013) Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi. New Phytol 197:1236–1249. https://doi.org/10.1111/nph.12085

    Article  CAS  PubMed  Google Scholar 

  48. Kubicek CP, Starr TL, Glass NL (2014) Plant cell wall-degrading enzymes and their secretion in plant-pathogenic fungi. Annu Rev Phytopathol 52:427–451. https://doi.org/10.1146/annurev-phyto-102313-045831

    Article  CAS  PubMed  Google Scholar 

  49. Kubo T, Terabayashi S, Takeda S, Sasaki H, Aburada M, Miyamoto KI (2006) Indoor cultivation and cultural characteristics of Wolfiporia cocos sclerotia using mushroom culture bottles. Biol Pharm Bull 29:1191–1196. https://doi.org/10.1248/bpb.29.1191

    Article  CAS  PubMed  Google Scholar 

  50. Barros L, Baptista P, Correia DM, Casal S, Oliveira B, Ferreira I (2007) Fatty acid and sugar compositions, and nutritional value of five wild edible mushrooms from Northeast Portugal. Food Chem 105:140–145. https://doi.org/10.1016/j.foodchem.2007.03.052

    Article  CAS  Google Scholar 

Download references

Funding

This research was funded by the National Key R&D Programme of China, grant number 2017YFC1703000 and the Hubei Province Technology Innovation Project (General Project), grant number 2020BCB035.

Author information

Authors and Affiliations

  1. College of Traditional Chinese Medicine, Hubei University of Chinese Medicine, No.16, West Huangjiahu Road, Hongshan District, Wuhan, 430065, Hubei, China

    Qi Wang, Bisheng Huang, Dahui Liu & Yuhuan Miao

  2. Hubei Provincial Hospital of Traditional Chinese Medicine, No.4, Huayuanshan Road, Wuchang District, Wuhan, 430071, Hubei, China

    Qi Wang

Authors
  1. Qi Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Bisheng Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Dahui Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yuhuan Miao
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Conceptualisation, B.-S.H.; data curation, Q.W. and D.L.; formal analysis, Q.W. and H.F.; funding acquisition, B.H.; investigation, Q.W., B.H., and D.L.; methodology, B.H. and H.F.; project administration, H.F.; resources, D.L.; validation, D.L. and Y.M.; writing – review & editing, Q.W., D.L., and Y.M. All authors have read and agreed to the published version of the manuscript.

Corresponding author

Correspondence to Bisheng Huang.

Ethics declarations

Conflict of interest

The authors declare that they have no competing interests.

Ethical Approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Rights and permissions

Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wang, Q., Huang, B., Liu, D. et al. Genome Resequencing and Transcriptome Analysis Reveal the Genetic Diversity of Wolfiporia cocos Germplasm and Genes Related to High Yield. Curr Microbiol 79, 312 (2022). https://doi.org/10.1007/s00284-022-03011-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00284-022-03011-3

Search

Navigation