The comparison of ITS-rDNA and tef1α genomic regions for phylogenetic study of some Trichoderma Species

Document Type : Research Paper

Authors

Department of Plant Protection, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran

Abstract

Genus Trichoderma is a monophyletic fungus which some their species is known as biocontrol agent. This study was carried out for phylogenetic analysis of some isolates of the genus Trichoderma. In this study 73 sequences (including 33 sequences from T. aspereluum, T. brevicompactum, T. capillare, T. harzianum, T. koningiopsis, T. pleuroticola and T. virens and 40 sequences obtained from GeneBank and ISTH) were used in phylogenetic analysis. The biomass of isolates grown in PDB was harvested by filter paper. The genomic DNA was extracted from mycelia after freeze-drying. The regions of ITS-rDNA, tef1/In2-3 and tef1/In4 were amplified using common and specific primers and then sequenced. The data analyzed using maximum likelihood (ML) algorithm through selecting the best-fitting nucleotide substitution model in MEGA 6 software. The results showed that all phylograms present relatively similar relationships for isolates among supported clades. In all gene trees except ITS-based phylogram, the isolates of T. koningiopsis and T. asperellum were positioned within a basal clade with strong bootstrap support. The tef1-based phylogeny showed a stronger supported clade for the species of T. brevicompactum, T.virens, T.koningiopsis and T.pleuroticola compere to ITS-based phylogeny. The tef1/In.4 based ML analysis generated supportive clade for Trichoderma isolates such as T. asperellum. This study confirms that tef1α/Intron4-based phylogeny provide reliable clustering for Trichoderma species.

Keywords

References

  1. Ainsworth, G.C. (1971). Ainsworth and Bisby’s Dictionary of the Fungi. 6th ed. Commonwealth Mycological Institute, Kew, Surrey, England. 663 pp.
  2. Chaverri, P., Castlebury, L.A., Overton, B.E. & Samuels, G.J. (2003). Hypocrea/Trichoderma: species with conidiophore elongations and green conidia. Mycologia, 95, 1100-1140.
  3. Crouse, J. & Amorese, D. (1987). Ethanol Precipitation: Ammonium Acetate as an Alternative to Sodium Acetate. Focus, 9, 3-5.
  4. Dodd, S., Crowhurst, R.N., Rodrigo, A.G., Samuels, G.J., Hill, R.A. & Stewart, A. (2003). Examination of Trichoderma phylogenies derived from ribosomal DNA sequence data. Mycological Research, 4, 32-39.
  5. Druzhinina, I. & Kubicek, C.P. (2005). Species concepts and biodiversity in Trichoderma and Hypocrea: from aggregate species to species clusters. Journal of Zhejiang University Science Botany, 6, 100-112.
  6. Druzhinina, I.S., Kopchinskiy, A.G. & Kubicek, C.P. (2006). The first 100 Trichoderma species characterized by molecular data. Mycoscience, 47, 55-64.
  7. Druzhinina, I.S., Kubicek, C.P., Komon-Zelazowska, M., Mulaw, T.B. & Bissett, J. (2010). The Trichoderma harzianum demon: complex speciation history resulting in coexistence of hypothetical biological species, recent agamospecies and numerous relict lineages. BMC Evolutionary Biology, 10, 94-94.
  8. Druzhinina, I.S., Komon-Zelazowska, M., Ismaiel, A., Jaklitsch, W., Mullaw, T., Samuels, G.J. & Kubicek, C.P. (2012). Molecular phylogeny and species delimitation in the section Longibrachiatum of Trichoderma. Fungal Genetics and Biology, 49, 358-368.
  9. Geiser, D.M., Jimenz Gasco, M.M., Kang, S., Mkalowska, I., Veeraraghavan, N., Ward, T.J., Zhang, N., Kuldau, G.A. & O’Donnell, K. (2004). Fusarium-IDv.1.0: A DNA sequence database for identifying Fusarium. European Journal of Plant Pathology, 110, 473-479.
  10. Gherbawy, Y., Druzhinina, I., Shaban, G.M., Wuczkowsky, M., Yaser, M., El-Naghy, M.A., Prillinger, H.J. & Kubicek, C.P. (2004). Trichoderma populations from alkaline agricultural soil in the Nile valley, Egypt, consist of only two species. Mycological Progress, 3, 211-218
  11. Hall, T.A. (1999).  BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95-98.
  12. Harman, G.E., Howell, C.R., Viterbo, A., Chet, I. & Lorito, M. (2004). Trichoderma species-opportunistic, avirulent plant symbionts. Nature Review Microbiology, 2, 43-56.
  13. Jaklitsch, W.M., Samuels, G.J., Dodd S.L., Lu, B.S. & Druzhinina, I.S.  (2006). Hypocrea rufa/Trichoderma viride: a reassessment, and description of five closely related species with and without warted conidia. Studies in Mycology, 56, 135-177.
  14. Kubicek, C.P., Bissett, J., Kullnig-Gradinger, C.M., Druzhinina, I.S. & Szakacs, G. (2003). Genetic and metabolic diversity of Trichoderma: a case study on South-East Asian isolates. Fungal Genetic and Biology, 38, 310-317.
  15. Kullnig-Gradinger, C., Szakacs, G. & Kubicek, C.P. (2002). Phylogeny and evolution of the genus Trichoderma: a multigene approach. Mycological Research, 106, 757-767.
  16. Mehrabi-Koushki, M., Rouhani, H. & Farsi, M. (2011).Genetic manipulation of fungal strains for Improvement of heterologous genes expression (a minireview). African Journal of Biotechnology, 10(41), 7939-7948.
  17. Mehrabi-Koushki, M., Rouhani, H., & Mahdikhani-Moghaddam, E. (2012). Differential display of abundantly expressed genes of Trichoderma harzianum during colonization of tomato-germinating seeds and roots. Current Microbiology, 65, 524-533.
  18. Naeimi, S., Khodaparast, S.A., Javan-Nikkhah, M., Vagvolgyi, Cs. & Kredics, L. (2011). Species patterns and phylogenetic relationships of Trichoderma strains in rice fields of southern Caspian Sea, Iran. Cereal Research Communication, 39, 560-568.
  19. Raeder, U. & Broda, P. (1985). Rapid preparation of DNA from filamentous fungi. Letters in Applied Microbiology, 1, 17-20.
  20. Samuels, G.J., Dodd, S.L., Gams, W., Castlebury, L.A. & Petrini, O. (2002). Trichoderma species associated with the green mold epidemic of commercially grown Agaricus bisporus. Mycologia, 94, 146-170.
  21. Samuels, G.J., Dodd, S., Lu, B.S., Petrini, O., Schroers, H.J. & Druzhinina, I. (2006). The Trichoderma koningii aggregate species. Studies in Mycology, 56, 67-133.
  22. Samuels, G.J., Ismaiel, A., Mulaw, T.B., Szakacs, G., Druzhinina, I.S., Kubicek, C.P. & Jaklitsch, W.M. (2012). The Longibrachiatum Clade of Trichoderma: a revision with new species. Fungal Diversity, 55, 77108.
  23. Shoukouhi, E. & Bissett, J. (2008). Preferred primers for sequencing the 50 end of the translation elongation factor 1-alpha gene (EF1-a1) and subunit 2 of the RNA polymerase B gene (RPB2). ISTH available from: http://www.isth.info/methods.
  24. Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution,30, 2725-2729.
  25. White, T.J., Bruns, T., Lee, S. & Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR Protocols: a guide to methods and applications. (Innis MA, Gelfand DH, Sninsky JJ, White TJ, eds). Academic Press, New York, USA: 315-322
  26. Zhang, C.L., Druzhinina, I.S., Kubicek, C.P. & Xu, T. (2005). Biodiversity of Trichoderma in China: evidence for a North to South difference of species distribution in East Asia. FEMS Microbiological Letter, 251, 251-257.
Iranian Journal of Plant Protection Science
Volume 47, Issue 1 - Serial Number 1
November 2016
Pages 61-70

Files

History

  • Receive Date: 14 September 2015
  • Revise Date: 06 April 2016
  • Accept Date: 04 May 2016

Share

How to cite

Statistics