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ITS2 RNA secondary structure analysis reveals close affinity between endophytic and pathogenic fungi: A case study in Fusarium species

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Abstract

Endophytes are microbes which colonize inner plant tissues without causing any disease symptoms. Many of the fungi isolated as endophytes show a close morphological resemblance to plant pathogenic fungi. It is commonly believed that pathogenic/non-pathogenic fungi become endophytic/pathogenic due to virulence loss/acquisition, respectively, but the molecular basis of such transformations and the shared characteristics are still to be elucidated. We have investigated the relationships between endophytes and pathogens based on internal transcribed spacer 2 (ITS2) sequence and secondary structure analyses in Fusarium as a model organism. We found that the ITS2 sequence-based phylogeny indicated close genetic proximity among endophytic and pathogenic strains of Fusarium species, suggesting that strains of this fungus can easily change between an endophytic and a necrotrophic lifestyle. We also observed a considerable discrepancy in the positions of bases in the ITS2 nucleotide sequences. RNA secondary structures of both endophytic and pathogenic forms of Fusarium were generated to distinguish between conserved and variable regions within the ITS2 sequence. The generated structures showed some structural similarities between the endophytic and pathogenic forms, with coincident variations in their respective junctions, hairpin loops, terminal loops and internal loops. Such findings suggest that Fusarium lifestyles are not stable but rather are dynamic and likely influenced by the genetic makeup of the fungal species, host factors and changing environment. Our research highlights the importance of the ITS2 sequence and its secondary structure as possible molecular markers to establish relationships and variations between the endophyte and pathogen lifestyle.

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Acknowledgments

The corresponding author gratefully acknowledges University Grants Commission (UGC), Govt. of India, for financial support in the form of an UGC Research Award.

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Authors and Affiliations

  1. Microbial Biotechnology Division, Department of Botany, North Orissa University, Baripada, 757003, Odisha, India

    Srichandan Padhi, Mrunmaya Kumar Panda, Devaranjan Das & Kumananda Tayung

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  1. Srichandan Padhi
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  2. Mrunmaya Kumar Panda
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  3. Devaranjan Das
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  4. Kumananda Tayung
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Correspondence to Kumananda Tayung.

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Padhi, S., Panda, M.K., Das, D. et al. ITS2 RNA secondary structure analysis reveals close affinity between endophytic and pathogenic fungi: A case study in Fusarium species. Ann Microbiol 66, 625–633 (2016). https://doi.org/10.1007/s13213-015-1142-x

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  • DOI: https://doi.org/10.1007/s13213-015-1142-x

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