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Whole RNA-sequencing and gene expression analysis of Trichoderma harzianum Tr-92 under chlamydospore-producing condition

  • Min Yuan
  • Yuanyuan Huang
  • Zhenhua Jia
  • Weina Ge
  • Lan Zhang
  • Qian Zhao
  • Shuishan Song
  • Yali HuangEmail author
Research Article
  • 47 Downloads

Abstract

Background

Trichoderma is one of the most important biocontrol fungi, which could produce mycelia, conidiospores, and chlamydospores three types of propagules under different conditions. Chlamydospores are produced in harsh conditions in various fungi, and may be more resistant to adverse conditions. However, the knowledge associated with the mechanism of chlamydospore formation remained unclear in Trichoderma.

Objectives

This study is aimed to explore the essential genes and regulatory pathways associated with chlamydospore formation in Trichoderma.

Methods

The culture condition, survival rate, and biocontrol effects of chlamydospores and conidiospores from Trichoderma.harzianum Tr-92 were determined. Furthermore, the whole transcriptome profiles of T. harzianum Tr-92 under chlamydospore-producing and chlamydospore-nonproducing conditions were performed.

Results

T. harzianum Tr-92 produced chlamydospores under particular conditions, and chlamydospore-based formulation of T. harzianum Tr-92 exhibited higher biocontrol ability against Botrytis cinerea in cucumber than conidoiospore-based formulation. In the transcriptome analysis, a total of 2,029 differentially expressed genes (DEGs) were identified in T. harzianum Tr-92 under chlamydospore-producing condition, compared to that under chlamydospore-nonproducing condition. GO classification indicated that the DEGs were significantly enriched in 284 terms among biological process, cellular components and molecular function categories. A total of 19 pathways were observed with DEGs by KEGG analysis. Furthermore, fifteen DEGs were verified by quantitative real-time PCR, and the expression profiles were consistent with the transcriptome data.

Conclusion

The results would provide a basis on the molecular mechanisms underlying Trichoderma sporulation, which would assist the development and application of fungal biocontrol agents.

Keywords

Trichoderma harzianum Biocontrol Conidiospores Chlamydospores Transcriptome sequencing Differentially expressed genes 

Notes

Acknowledgements

This work was supported by the National Key Research and Development program of China “Topsoil regulation and soil fertility improvement of the wheat-maize field in northern of Huang-Huai-Hai” (2017YFD0300905), the Key Fundamental Research Program of Hebei Province (15962904D), the National Water Pollution Control and Treatment Science and Technology Major Project of China (2015ZX07204-007), and National Natural Science Foundation of China (31401212).

Compliance with ethical standards

Conflict of interest

The authors declare that they do not have conflict of interest.

Research involving human and animal rights

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

Supplementary material

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References

  1. Blaszczyk L, Basinska-Barczak A et al (2017) Suppressive effect of Trichoderma spp. on toxigenic Fusarium species. Pol J Microbiol 66(1):85–100CrossRefGoogle Scholar
  2. Bottcher B, Pollath C et al (2016) Candida species Rewired hyphae developmental programs for chlamydospore formation. Front Microbiol 7:1697CrossRefGoogle Scholar
  3. Campanha NH, Neppelenbroek KH et al (2005) Phenotypic methods and commercial systems for the discrimination between C. albicans and C. dubliniensis. Oral Dis 11(6):392–398CrossRefGoogle Scholar
  4. Carruthers M, Yurchenko AA et al (2018) De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species. BMC Genom 19(1):32CrossRefGoogle Scholar
  5. Choudhri P, Rani M et al (2018) De novo sequencing, assembly and characterisation of Aloe vera transcriptome and analysis of expression profiles of genes related to saponin and anthraquinone metabolism. BMC Genom 19(1):427CrossRefGoogle Scholar
  6. Deng JJ, Huang WQ et al (2018) Biocontrol activity of recombinant aspartic protease from Trichoderma harzianum against pathogenic fungi. Enzyme Microb Technol 112:35–42CrossRefGoogle Scholar
  7. Eyal J, Baker CP et al (1997) Large-scale production of chlamydospores of Gliocladium virens strain GL-21 in submerged culture. J Ind Microbiol Biotechnol 19(3):163–168CrossRefGoogle Scholar
  8. Fay JV, Watkins CJ et al (2018) Yerba mate (Ilex paraguariensis. A. St.-Hil.) de novo transcriptome assembly based on tissue specific genomic expression profiles. BMC Genom 19(1):891CrossRefGoogle Scholar
  9. Fravel DR (2005) Commercialization and implementation of biocontrol. Annu Rev Phytopathol 43:337–359CrossRefGoogle Scholar
  10. Fu L, Niu B et al (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28(23):3150–3152CrossRefGoogle Scholar
  11. Giosa D, Felice MR et al (2017) Whole RNA-sequencing and transcriptome assembly of Candida albicans and Candida africana under chlamydospore-inducing conditions. Genome Biol Evol 9(7):1971–1977CrossRefGoogle Scholar
  12. Grabherr MG, Haas BJ et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29(7):644–652CrossRefGoogle Scholar
  13. Harel YM, Mehari ZH et al (2014) Systemic resistance to gray mold induced in tomato by benzothiadiazole and Trichoderma harzianum T39. Phytopathology 104(2):150–157CrossRefGoogle Scholar
  14. Harman GE (2000) Myths and dogmas of biocontrol changes in perceptions derived from research on Trichoderma harzinum T-22. Plant Dis 84(4):377–393CrossRefGoogle Scholar
  15. Harman GE (2006) Overview of Mechanisms and uses of Trichoderma spp. Phytopathology 96(2):190–194CrossRefGoogle Scholar
  16. Harman GE, Howell CR et al (2004) Trichoderma species—opportunistic, avirulent plant symbionts. Nat Rev Microbiol 2(1):43–56CrossRefGoogle Scholar
  17. Kim SH, Vujanovic V (2016) Relationship between mycoparasites lifestyles and biocontrol behaviors against Fusarium spp. and mycotoxins production. Appl Microbiol Biotechnol 100(12):5257–5272CrossRefGoogle Scholar
  18. Li Y, Sun R et al (2016a) Antagonistic and biocontrol potential of Trichoderma asperellum ZJSX5003 against the maize stalk rot pathogen Fusarium graminearum. Indian J Microbiol 56(3):318–327CrossRefGoogle Scholar
  19. Li YQ, Song K et al (2016b) Statistical culture-based strategies to enhance chlamydospore production by Trichoderma harzianum SH2303 in liquid fermentation. J Zhejiang Univ Sci B 17(8):619–627CrossRefGoogle Scholar
  20. Martinez-Medina A, Fernandez I et al (2013) Deciphering the hormonal signalling network behind the systemic resistance induced by Trichoderma harzianum in tomato. Front Plant Sci 4:206CrossRefGoogle Scholar
  21. Martinez-Nunez L, Riquelme M (2015) Role of BGT-1 and BGT-2, two predicted GPI-anchored glycoside hydrolases/glycosyltransferases, in cell wall remodeling in Neurospora crassa. Fungal Genet Biol 85:58–70CrossRefGoogle Scholar
  22. Ment D, Gindin G et al (2010) The effect of temperature and relative humidity on the formation of Metarhizium anisopliae chlamydospores in tick eggs. Fungal Biol 114(1):49–56CrossRefGoogle Scholar
  23. Mishra DS, Prajapati CR et al (2012) Relative bio-efficacy and shelf-life of mycelial fragments, conidia and chlamydospores of Trichoderma harzianum. Vegetos 25(1):225–232Google Scholar
  24. Moran GP, MacCallum DM et al (2007) Differential regulation of the transcriptional repressor NRG1 accounts for altered host-cell interactions in Candida albicans and Candida dubliniensis. Mol Microbiol 66(4):915–929CrossRefGoogle Scholar
  25. Mortazavi A, Williams BA et al (2008) Mapping and quantifying mammalian transcriptomes by RNA-SEq. Nat Methods 5(7):621–628CrossRefGoogle Scholar
  26. Noble SM, Gianetti BA et al (2017) Candida albicans cell-type switching and functional plasticity in the mammalian host. Nat Rev Microbiol 15(2):96–108CrossRefGoogle Scholar
  27. O’Connor L, Caplice N et al (2010) Differential filamentation of Candida albicans and Candida dubliniensis Is governed by nutrient regulation of UME6 expression. Eukaryot Cell 9(9):1383–1397CrossRefGoogle Scholar
  28. Palige K, Linde J et al (2013) Global transcriptome sequencing identifies chlamydospore specific markers in Candida albicans and Candida dubliniensis. PLoS One 8(4):e61940CrossRefGoogle Scholar
  29. Rai S, Kashyap PL et al (2016) Identification, characterization and phylogenetic analysis of antifungal Trichoderma from tomato rhizosphere. Springerplus 5(1): 1939Google Scholar
  30. Shoresh M, Harman GE et al (2010) Induced systemic resistance and plant responses to fungal biocontrol agents. Annu Rev Phytopathol 48:21–43CrossRefGoogle Scholar
  31. Staib P, Morschhauser J (2007) Chlamydospore formation in Candida albicans and Candida dubliniensis—an enigmatic developmental programme. Mycoses 50(1):1–12CrossRefGoogle Scholar
  32. Steindorff AS, Ramada MH et al (2014) Identification of mycoparasitism-related genes against the phytopathogen Sclerotinia sclerotiorum through transcriptome and expression profile analysis in Trichoderma harzianum. BMC Genom 15:204CrossRefGoogle Scholar
  33. Sun ZB, Zhang J et al (2018) Identification of genes related to chlamydospore formation in Clonostachys rosea 67-1. Microbiologyopen 8(1):e00624CrossRefGoogle Scholar
  34. Swaminathan J, van Koten C et al (2016) Formulations for delivering Trichoderma atroviridae spores as seed coatings, effects of temperature and relative humidity on storage stability. J Appl Microbiol 120(2):425–431CrossRefGoogle Scholar
  35. Tzelepis G, Dubey M et al (2015) Identifying glycoside hydrolase family 18 genes in the mycoparasitic fungal species Clonostachys rosea. Microbiology 161(7):1407–1419CrossRefGoogle Scholar
  36. Verma M, Brar SK et al (2007) Antagonistic fungi, Trichoderma spp.: panoply of biological control. Biochem Eng J 37(1):1–20CrossRefGoogle Scholar
  37. Vos CM, De Cremer K et al (2015) The toolbox of Trichoderma spp. in the biocontrol of Botrytis cinerea disease. Mol Plant Pathol 16(4):400–412CrossRefGoogle Scholar
  38. Whiteway M, Bachewich C (2007) Morphogenesis in Candida albicans. Annu Rev Microbiol 61:529–553CrossRefGoogle Scholar
  39. Yuan M, Huang Y et al (2019) Involvement of jasmonic acid, ethylene and salicylic acid signaling pathways behind the systemic resistance induced by Trichoderma longibrachiatum H9 in cucumber. BMC Genom 20(1):144CrossRefGoogle Scholar
  40. Zhang J, Sun Z et al (2017) Identification of suitable reference genes during the formation of chlamydospores in Clonostachys rosea 67-1. Microbiologyopen 6(5):e00505CrossRefGoogle Scholar

Copyright information

© The Genetics Society of Korea 2019

Authors and Affiliations

  • Min Yuan
    • 1
  • Yuanyuan Huang
    • 2
  • Zhenhua Jia
    • 2
  • Weina Ge
    • 1
  • Lan Zhang
    • 1
  • Qian Zhao
    • 2
  • Shuishan Song
    • 2
  • Yali Huang
    • 2
    Email author
  1. 1.College of Life SciencesNorth China University of Science and TechnologyTangshanPeople’s Republic of China
  2. 2.Biology InstituteHebei Academy of SciencesShijiazhuangPeople’s Republic of China

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