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

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Mehrabi Koushki Mehdi; Bavarsad Maryam; Farrokhinejad Reza; Jamshid Mehdi; Alimohammadi Ashkan

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Journal: Iranian Journal of Plant Protection Science Year:2016 | Volume:47 | Issue:1 Page(s): 61-70

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Title

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

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Keywords

ITSQ1

maximum likelihoodQ2

tef1αQ1

TrichodermaQ1

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.

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APA: Copy

Mehrabi Koushki, Mehdi, Farrokhinejad, Reza, Jamshid, Mehdi, Alimohammadi, Ashkan, & Bavarsad, Maryam. (2016). The comparison of ITS-rDNA and tef1α genomic regions for phylogenetic study of some Trichoderma Species. IRANIAN JOURNAL OF PLANT PROTECTION SCIENCE (IRANIAN JOURNAL OF AGRICULTURAL SCIENCES), 47(1 ), 61-70. SID. https://sid.ir/paper/171572/en

Vancouver: Copy

Mehrabi Koushki Mehdi, Farrokhinejad Reza, Jamshid Mehdi, Alimohammadi Ashkan, Bavarsad Maryam. The comparison of ITS-rDNA and tef1α genomic regions for phylogenetic study of some Trichoderma Species. IRANIAN JOURNAL OF PLANT PROTECTION SCIENCE (IRANIAN JOURNAL OF AGRICULTURAL SCIENCES)[Internet]. 2016;47(1 ):61-70. Available from: https://sid.ir/paper/171572/en

IEEE: Copy

Mehdi Mehrabi Koushki, Reza Farrokhinejad, Mehdi Jamshid, Ashkan Alimohammadi, and Maryam Bavarsad, “The comparison of ITS-rDNA and tef1α genomic regions for phylogenetic study of some Trichoderma Species,” IRANIAN JOURNAL OF PLANT PROTECTION SCIENCE (IRANIAN JOURNAL OF AGRICULTURAL SCIENCES), vol. 47, no. 1 , pp. 61–70, 2016, [Online]. Available: https://sid.ir/paper/171572/en

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