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Molecular phylogeny of plant pathogenic fungi based on start codon targeted (SCoT) polymorphism

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Abstract

Background

A number of molecular marker systems have been developed to assess genetic diversity, carry out phylogenetic analysis, and diagnose and discriminate plant pathogenic fungi. The start codon targeted (SCoT) markers system is a novel approach used here to investigate intra and interspecific polymorphisms of phytopathogenic fungi.

Materials and methods

This study assessed genetic variability between and within 96 isolates of ten fungal species associated with a variety of plant species using 36 SCoT primers.

Results

The six primers generated 331 distinct and reproducible banding patterns, of which 322 were polymorphic (97.28%), resulting in 53.67 polymorphic bands per primer. All primers produced informative amplification profiles that distinguished all fungal species. With a resolving power of 10.65, SCoT primer 12 showed the highest polymorphism among species, followed by primer 33 and primer 29. Polymorphic loci (PPL), Nei’s diversity index (h), and Shannon index (I) percentages were 6.25, 0.018, and 0.028, respectively. UPGMA analysis separated all isolates based on morphological classification and revealed significant genetic variation among fungal isolates at the intraspecific level. PCoA analysis strongly supported fungal species discrimination and genetic variation. The other parameters of evaluation proved that SCoT markers are at least as effective as other DNA markers.

Conclusions

SCoT markers were effective in identifying plant pathogenic fungi and were a powerful tool for estimating genetic variation and population structure of different fungi species.

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Data availability

The data that support the findings of this study are available from the corresponding author upon reasonable request.

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Funding

The authors would like to thank the Şırnak University Scientific Research Projects Coordination Unit for its financial support under project code 2021.FNAP.13.02.02.

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Authors and Affiliations

  1. Department of Plant Protection, Faculty of Agriculture, Şırnak University, Şırnak, Turkey

    Gülsüm Palacıoğlu

  2. Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey

    Mehtap Alkan & Göksel Özer

  3. Department of Plant and Animal Production, Vocational School of Kızıltepe, Mardin Artuklu University, Mardin, Turkey

    Sibel Derviş

  4. Department of Plant Protection, Faculty of Agriculture, Ankara University, Ankara, Turkey

    Harun Bayraktar

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  1. Gülsüm Palacıoğlu
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Contributions

GP; Investigation, methodology, resource management, writing-first draft preparation, and formal analysis. MA; Investigation, methodology, and visualization. SD: Investigation and editing. HB; Supervision, writing, and editing. GÖ; Investigation, supervision, resource management, and formal analysis.

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Correspondence to Harun Bayraktar.

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Palacıoğlu, G., Alkan, M., Derviş, S. et al. Molecular phylogeny of plant pathogenic fungi based on start codon targeted (SCoT) polymorphism. Mol Biol Rep 50, 8271–8279 (2023). https://doi.org/10.1007/s11033-023-08735-4

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