Araştırma Makalesi
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CHARACTERIZATION OF cox3 AND rnl GENES ENCODED IN MITOCHONDRIA OF Fusarium graminearum Schwabe

Yıl 2023, Cilt: 24 Sayı: 1, 3 - 9, 15.04.2023
https://doi.org/10.23902/trkjnat.1144980

Öz

In this study, the phylogenetic relationship among Fusarium graminearum Schwabe isolates was established for the first time based on mitochondrial cox3 and rnl gene variations. The genes were amplified from 45 isolates purified from Türkiye and Iran together with 2 Korean strains by polymerase chain reaction. The amplicons were sequenced and nucleotide polymorphisms were detected by alignment. The phylogenetic relationship was constructed by using PAUP 4.0a with the maximum parsimony method. Fragments with 477 bp length, belonging to cox3, were obtained from 46 samples; 1547 bp-amplicons of rnl were produced from 45 samples. Sequence similarities were calculated as 30-100 % and 17-94 % for cox3 and rnl, respectively. Nucleotide variations within the rnl was found higher than within cox3. It was shown that SNPs and in-dels, found in coding regions, cause a codon change and may alter more than one codon by causing frame shift without affect gene functions. Bootstrap values belonging to cox3 and rnl dataset was found ranging from 57 to 84 %, and 54 to 100 %, respectively. Parsimony analysis revealed that Korean isolates were in monophyletic relationship with Turkish and Iranian isolates. It is proposed that the methodology can be applied to other fungal species because the phylogenetic relationships at the intraspecific level are able to establish among Fusarium species based on mitochondrial gene variation.

Destekleyen Kurum

Research Found of İstanbul University

Proje Numarası

43153

Teşekkür

The authors thank to Prof. Dr. Berna Tunali (Department of Plant Protection, Agricultural Faculty, Ondokuz Mayıs University, Samsun, Türkiye), Prof. Dr. Bahram Sharifnabi (Department of Plant Protection, College of Agriculture, Isfahan University of Technology, Isfahan, Iran) and Dr. Theresa Lee (Department of Agro-Food Safety and Crop Protection, National Institute of Agricultural Sciences, Wanju, South Korea) for providing the fungal material.

Kaynakça

  • 1. Abboud, T.G., Zubaer, A. & Wai, A. 2018. The complete mitochondrial genome of the Dutch elm disease fungus Ophiostoma novoulmi subsp. novo-ulmi. Canadian Journal of Microbiology, (64)5: 1-10.
  • 2. Alexeyev, M., Shokolenko, I. & Wilson, G. 2013. The maintenance of mitochondrial DNA integrity - Critical analysis and update. Cold Spring Harbor Perspectives in Biology, 5(5): 1-10.
  • 3. Al-Reedy, R.M., Malireddy, R. & Dillman, C.B. 2012. Comparative analysis of Fusarium mitochondrial genomes reveals a highly variable that encodes an exceptionally open reading frame, Fungal Genetics and Biology, 4: 1-14.
  • 4. Avise, J.C. & Sep, N. 1989. Gene Trees and Organismal Histories: A Phylogenetic Approach to Population Biology. Evolution, 43(6): 1192-1208.
  • 5. Bietenhader, M., Martos, A. & Tetaud, E. 2012. Experimental relocation of the mitochondrial atp9 gene to the nucleus reveals forces underlying mitochondrial genome evolution. PLoS Genetics, (8)8: 1-15.
  • 6. Brankovics, B., Kulik T. & Sawicki, J. 2018. First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes, Physical Chemistry, 6: e5963.
  • 7. Brown, W.M., George M. & Wilson, A.C. 1979. Rapid evolution of animal mitochondrial DNA. PNAS Genetics, 76(4): 1967-1971.
  • 8. Déquard-Chablet, M., Sellam, C., H., Golik, P. & Bidard, F. 2011. Two nuclear life cycle-regulated genes encode interchangeable subunits c of mitochondrial ATP synthase in Podospora anserine. Molecular Biology and Evolution, (28)7: 2063-2075.
  • 9. Fitzpatrick, D.A. 2012. Horizontal gene transfer in fungi. FEMS Microbiology Letters, 329(1): 1-8.
  • 10. Funk, E.R., Adams, A.N. & Spotten, S.M. 2018. The complete mitochondrial genomes of five lichenized fungi in the genus Usnea (Ascomycota: Parmeliaceae). Mitochondrial DNA Part B: Reseources, 3(1): 305-308.
  • 11. Goswami, R.S. & Kistler, C. 2004. Heading for disaster: Fusarium graminearum in cereal crops. Molecular Plant Pathology, 5(6): 515-525.
  • 12. Gray, M.W. 1999. Evolution of organellar genomes. Current Opinion in Genetics and Development, (9)6: 678-687.
  • 13. Haltia, T., Saraste, M. & Wikström, M. 1991. Subunit III of cytochrome c oxidase is not involved in proton translocation: a site-directed mutagenesis study. The EMBO Journal, (10)8: 2015-2021.
  • 14. Hao, J.J., Xie, S.N. & Sun, J. 2017. Analysis of Fusarium graminearum Species Complex from Wheat–Maize Rotation Regions in Henan (China). Plant Diseases, 101(5): 720-725.
  • 15. Hausner, G. 2003. Fungal mitochondrial genomes, plasmids and introns. Applied Microbiology and Biotechnology, 3(C): 101-131.
  • 16. Hensgens, L.A.M., Grivel, L.A. & Borst. P., 1979. Nucleotide sequence of the mitochondrial structural gene for subunit 9 of yeast ATPase complex. Proceedings of the National Academy of Sciences of the United States of America, (76)4: 1663-1667.
  • 17. Jeanmougin, F., Thompson, J.D. & Gouy, M. 1998. Multiple sequence alignment with Clustal X. Trends in Biochemical Sciences, 23(10): 403-405.
  • 18. Kim, D.H., Martyn, D. & Magill, C.W. 1993. Mitochondrial DNA (mtDNA) relatedness among formae speciales of Fusarium oxysporum in the Cucurbitaceae. Genetics, 83(1): 91-97.
  • 19. Kim, D.H. 1992. Restriction length polymorphism groups and physical map of mitochondrial DNA from Fusarium oxysporum f. sp. niveum. Phytopathology, 82: 346-353.
  • 20. Kistler, H., Bosland, P.W., Benny, U., Leong, S. & Williams, P.H. 1987. Relatedness of strains of Fusarium oxysporum from crucifers measured by examination of mitochondrial and ribosomal DNA. Phytopathology, 77: 1289-1293.
  • 21. Kistler, H.C. 2008. Relatedness of Strains of Fusarium oxysporum from Crucifers Measured by Examination of Mitochondrial and Ribosomal DNA. Phytopathology, 77(9): 1289-1298.
  • 22. Kulik, T., Brankovics, B. & van Diepeningen, A.D. 2020. Diversity of mobile genetic elements in the mitogenomes of closely related Fusarium culmorum and F. graminearum sensu stricto strains and its implication for diagnostic purposes. Frontiers in Microbiology, 11: 1002-1016.
  • 23. Láday, M., Juhász, Á., Mulè, G., Moretti, A., Szécsi, Á. & Logrieco, A. 2004. Mitochondrial DNA diversity and lineage determination of European isolates of Fusarium graminearum (Gibberella zeae). European Journal of Plant Pathology, 110(5-6): 545-550.
  • 24. Larkin, M.A., Blackshields, G. & Brown, N.P. 2007. Clustal W and Clustal X version 2.0. Bioinformatics, 23(21): 2947-2948.
  • 25. Lee, T., Paek, J.S. & Lee, K.A. 2016. Occurrence of toxigenic Fusarium vorosii among small grain cereals in Korea. Plant Pathology Journal, 32(5): 407-413.
  • 26. Sarver, B.A.J., Ward, T.J. & Gale, L.R. 2011. Novel Fusarium head blight pathogens from Nepal and Louisiana revealed by multilocus genealogical concordance. Fungal Genetics and Biology, 48: 1096-1107.
  • 27. Starkey, D.E., Ward, T.J. & Aoki, T. 2007. Global molecular surveillance reveals novel Fusarium head blight species and trichothecene toxin diversity. Fungal Genetics and Biology, 44(11): 1191-1204.
  • 28. Swofford, D.L. 2004. PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4. Journal of Molecular Evolution, 42(2): 294-307.
  • 29. Taylor, J.W., Jacobson, D.J. & Kroken, S. 2000. Phylogenetic species recognition and species concepts in fungi. Fungal Genetics and Biology, 31(1): 21-32.
  • 30. Westermann, B. 2012. Mitochondrial fusion and fission in cell life and death. Nature Reviews Molecular Cell Biology, 11(12): 872-884.
  • 31. Westermann, B. & Prokisch, H. 2002. Mitochondrial dynamics in filamentous fungi. Fungal Genetics and Biology, 36: 91-97.
  • 32. Wiebe, M.G. 2003. Stable production of recombinant proteins in filamentous fungi-problems and improvements. Mycologist, 17(3): 140-144.
  • 33. Yang, M., Zhang, H. & van der Lee, T.A.J. 2020. Population Genomic Analysis Reveals a Highly Conserved Mitochondrial Genome in Fusarium asiaticum, Frontiers in Microbiology, 11: 839-852.
  • 34. Yli-Mattila, T., Gagkaeva, T. & Ward, T.J. 2009. A novel Asian clade within the Fusarium graminearum species complex includes a newly discovered cereal head blight pathogen from the Russian Far East. Mycologia, 101(6): 841-852.
Yıl 2023, Cilt: 24 Sayı: 1, 3 - 9, 15.04.2023
https://doi.org/10.23902/trkjnat.1144980

Öz

Bu çalışmada, mitokondriyal cox3 ve rnl genlerinin varyasyonlarına dayalı olarak Fusarium graminearum izolatları arasındaki filogenetik ilişki ilk kez ortaya kondu. cox3 ve rnl genleri polimeraz zincir reaksiyonu ile 2 Kore suşu ile Türkiye ve İran'dan saflaştırılan 45 izolattan çoğaltıldı. Amplikonlar dizilendi ve hizalama analizleri ile nükleotid polimorfizmleri tespit edildi. Filogenetik ilişki, maksimum tutumluluk yöntemiyle PAUP 4.0a programı kullanılarak oluşturuldu. 46 örnekten cox3'e ait 477 bp uzunluğunda fragmentler çoğaltılırken; rnl genine ait 1547 bp-amplikon 45 örnekten çoğaltıldı. cox3 ve rnl için dizi benzerlikleri sırasıyla %30-100 ve %17-94 aralığında hesaplandı. rnl gen bölgesinde, cox3’e kıyasla nukleotid varyasyonlarının daha yüksek oranda taşındığı belirlendi. Kodlama bölgelerinde bulunan SNP'lerin ve in-del'lerin gen fonksiyonlarını etkilemeden çerçeve kaymasına neden olduğu ve bu varyasyonların birden fazla kodonu değiştirebildiği belirlendi. Filogenetik analizlerle hesaplanan cox3 ve rnl veri setine ait bootstrap değerleri sırasıyla %57 ile %84 ve %54 ile %100 arasında hesaplandı. Parsimoni analizi, Kore izolatlarının Türk ve İran izolatları ile monofiletik ilişki içinde olduğunu ortaya koydu. Fusarium’da tür içi filogenetik ilişkilerin mitokondriyal gen varyasyonuna dayalı olarak belirlenebilmesi nedeniyle yöntemin diğer mantar türlerine de uygulanabileceği önerilmektedir.

Proje Numarası

43153

Kaynakça

  • 1. Abboud, T.G., Zubaer, A. & Wai, A. 2018. The complete mitochondrial genome of the Dutch elm disease fungus Ophiostoma novoulmi subsp. novo-ulmi. Canadian Journal of Microbiology, (64)5: 1-10.
  • 2. Alexeyev, M., Shokolenko, I. & Wilson, G. 2013. The maintenance of mitochondrial DNA integrity - Critical analysis and update. Cold Spring Harbor Perspectives in Biology, 5(5): 1-10.
  • 3. Al-Reedy, R.M., Malireddy, R. & Dillman, C.B. 2012. Comparative analysis of Fusarium mitochondrial genomes reveals a highly variable that encodes an exceptionally open reading frame, Fungal Genetics and Biology, 4: 1-14.
  • 4. Avise, J.C. & Sep, N. 1989. Gene Trees and Organismal Histories: A Phylogenetic Approach to Population Biology. Evolution, 43(6): 1192-1208.
  • 5. Bietenhader, M., Martos, A. & Tetaud, E. 2012. Experimental relocation of the mitochondrial atp9 gene to the nucleus reveals forces underlying mitochondrial genome evolution. PLoS Genetics, (8)8: 1-15.
  • 6. Brankovics, B., Kulik T. & Sawicki, J. 2018. First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes, Physical Chemistry, 6: e5963.
  • 7. Brown, W.M., George M. & Wilson, A.C. 1979. Rapid evolution of animal mitochondrial DNA. PNAS Genetics, 76(4): 1967-1971.
  • 8. Déquard-Chablet, M., Sellam, C., H., Golik, P. & Bidard, F. 2011. Two nuclear life cycle-regulated genes encode interchangeable subunits c of mitochondrial ATP synthase in Podospora anserine. Molecular Biology and Evolution, (28)7: 2063-2075.
  • 9. Fitzpatrick, D.A. 2012. Horizontal gene transfer in fungi. FEMS Microbiology Letters, 329(1): 1-8.
  • 10. Funk, E.R., Adams, A.N. & Spotten, S.M. 2018. The complete mitochondrial genomes of five lichenized fungi in the genus Usnea (Ascomycota: Parmeliaceae). Mitochondrial DNA Part B: Reseources, 3(1): 305-308.
  • 11. Goswami, R.S. & Kistler, C. 2004. Heading for disaster: Fusarium graminearum in cereal crops. Molecular Plant Pathology, 5(6): 515-525.
  • 12. Gray, M.W. 1999. Evolution of organellar genomes. Current Opinion in Genetics and Development, (9)6: 678-687.
  • 13. Haltia, T., Saraste, M. & Wikström, M. 1991. Subunit III of cytochrome c oxidase is not involved in proton translocation: a site-directed mutagenesis study. The EMBO Journal, (10)8: 2015-2021.
  • 14. Hao, J.J., Xie, S.N. & Sun, J. 2017. Analysis of Fusarium graminearum Species Complex from Wheat–Maize Rotation Regions in Henan (China). Plant Diseases, 101(5): 720-725.
  • 15. Hausner, G. 2003. Fungal mitochondrial genomes, plasmids and introns. Applied Microbiology and Biotechnology, 3(C): 101-131.
  • 16. Hensgens, L.A.M., Grivel, L.A. & Borst. P., 1979. Nucleotide sequence of the mitochondrial structural gene for subunit 9 of yeast ATPase complex. Proceedings of the National Academy of Sciences of the United States of America, (76)4: 1663-1667.
  • 17. Jeanmougin, F., Thompson, J.D. & Gouy, M. 1998. Multiple sequence alignment with Clustal X. Trends in Biochemical Sciences, 23(10): 403-405.
  • 18. Kim, D.H., Martyn, D. & Magill, C.W. 1993. Mitochondrial DNA (mtDNA) relatedness among formae speciales of Fusarium oxysporum in the Cucurbitaceae. Genetics, 83(1): 91-97.
  • 19. Kim, D.H. 1992. Restriction length polymorphism groups and physical map of mitochondrial DNA from Fusarium oxysporum f. sp. niveum. Phytopathology, 82: 346-353.
  • 20. Kistler, H., Bosland, P.W., Benny, U., Leong, S. & Williams, P.H. 1987. Relatedness of strains of Fusarium oxysporum from crucifers measured by examination of mitochondrial and ribosomal DNA. Phytopathology, 77: 1289-1293.
  • 21. Kistler, H.C. 2008. Relatedness of Strains of Fusarium oxysporum from Crucifers Measured by Examination of Mitochondrial and Ribosomal DNA. Phytopathology, 77(9): 1289-1298.
  • 22. Kulik, T., Brankovics, B. & van Diepeningen, A.D. 2020. Diversity of mobile genetic elements in the mitogenomes of closely related Fusarium culmorum and F. graminearum sensu stricto strains and its implication for diagnostic purposes. Frontiers in Microbiology, 11: 1002-1016.
  • 23. Láday, M., Juhász, Á., Mulè, G., Moretti, A., Szécsi, Á. & Logrieco, A. 2004. Mitochondrial DNA diversity and lineage determination of European isolates of Fusarium graminearum (Gibberella zeae). European Journal of Plant Pathology, 110(5-6): 545-550.
  • 24. Larkin, M.A., Blackshields, G. & Brown, N.P. 2007. Clustal W and Clustal X version 2.0. Bioinformatics, 23(21): 2947-2948.
  • 25. Lee, T., Paek, J.S. & Lee, K.A. 2016. Occurrence of toxigenic Fusarium vorosii among small grain cereals in Korea. Plant Pathology Journal, 32(5): 407-413.
  • 26. Sarver, B.A.J., Ward, T.J. & Gale, L.R. 2011. Novel Fusarium head blight pathogens from Nepal and Louisiana revealed by multilocus genealogical concordance. Fungal Genetics and Biology, 48: 1096-1107.
  • 27. Starkey, D.E., Ward, T.J. & Aoki, T. 2007. Global molecular surveillance reveals novel Fusarium head blight species and trichothecene toxin diversity. Fungal Genetics and Biology, 44(11): 1191-1204.
  • 28. Swofford, D.L. 2004. PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4. Journal of Molecular Evolution, 42(2): 294-307.
  • 29. Taylor, J.W., Jacobson, D.J. & Kroken, S. 2000. Phylogenetic species recognition and species concepts in fungi. Fungal Genetics and Biology, 31(1): 21-32.
  • 30. Westermann, B. 2012. Mitochondrial fusion and fission in cell life and death. Nature Reviews Molecular Cell Biology, 11(12): 872-884.
  • 31. Westermann, B. & Prokisch, H. 2002. Mitochondrial dynamics in filamentous fungi. Fungal Genetics and Biology, 36: 91-97.
  • 32. Wiebe, M.G. 2003. Stable production of recombinant proteins in filamentous fungi-problems and improvements. Mycologist, 17(3): 140-144.
  • 33. Yang, M., Zhang, H. & van der Lee, T.A.J. 2020. Population Genomic Analysis Reveals a Highly Conserved Mitochondrial Genome in Fusarium asiaticum, Frontiers in Microbiology, 11: 839-852.
  • 34. Yli-Mattila, T., Gagkaeva, T. & Ward, T.J. 2009. A novel Asian clade within the Fusarium graminearum species complex includes a newly discovered cereal head blight pathogen from the Russian Far East. Mycologia, 101(6): 841-852.
Toplam 34 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Konular Genetik
Bölüm Araştırma Makalesi/Research Article
Yazarlar

Aylin Gazdağlı 0000-0002-7011-8640

Gülruh Albayrak 0000-0002-4499-8912

Proje Numarası 43153
Yayımlanma Tarihi 15 Nisan 2023
Gönderilme Tarihi 18 Temmuz 2022
Kabul Tarihi 26 Ekim 2022
Yayımlandığı Sayı Yıl 2023 Cilt: 24 Sayı: 1

Kaynak Göster

APA Gazdağlı, A., & Albayrak, G. (2023). CHARACTERIZATION OF cox3 AND rnl GENES ENCODED IN MITOCHONDRIA OF Fusarium graminearum Schwabe. Trakya University Journal of Natural Sciences, 24(1), 3-9. https://doi.org/10.23902/trkjnat.1144980
AMA Gazdağlı A, Albayrak G. CHARACTERIZATION OF cox3 AND rnl GENES ENCODED IN MITOCHONDRIA OF Fusarium graminearum Schwabe. Trakya Univ J Nat Sci. Nisan 2023;24(1):3-9. doi:10.23902/trkjnat.1144980
Chicago Gazdağlı, Aylin, ve Gülruh Albayrak. “CHARACTERIZATION OF Cox3 AND Rnl GENES ENCODED IN MITOCHONDRIA OF Fusarium Graminearum Schwabe”. Trakya University Journal of Natural Sciences 24, sy. 1 (Nisan 2023): 3-9. https://doi.org/10.23902/trkjnat.1144980.
EndNote Gazdağlı A, Albayrak G (01 Nisan 2023) CHARACTERIZATION OF cox3 AND rnl GENES ENCODED IN MITOCHONDRIA OF Fusarium graminearum Schwabe. Trakya University Journal of Natural Sciences 24 1 3–9.
IEEE A. Gazdağlı ve G. Albayrak, “CHARACTERIZATION OF cox3 AND rnl GENES ENCODED IN MITOCHONDRIA OF Fusarium graminearum Schwabe”, Trakya Univ J Nat Sci, c. 24, sy. 1, ss. 3–9, 2023, doi: 10.23902/trkjnat.1144980.
ISNAD Gazdağlı, Aylin - Albayrak, Gülruh. “CHARACTERIZATION OF Cox3 AND Rnl GENES ENCODED IN MITOCHONDRIA OF Fusarium Graminearum Schwabe”. Trakya University Journal of Natural Sciences 24/1 (Nisan 2023), 3-9. https://doi.org/10.23902/trkjnat.1144980.
JAMA Gazdağlı A, Albayrak G. CHARACTERIZATION OF cox3 AND rnl GENES ENCODED IN MITOCHONDRIA OF Fusarium graminearum Schwabe. Trakya Univ J Nat Sci. 2023;24:3–9.
MLA Gazdağlı, Aylin ve Gülruh Albayrak. “CHARACTERIZATION OF Cox3 AND Rnl GENES ENCODED IN MITOCHONDRIA OF Fusarium Graminearum Schwabe”. Trakya University Journal of Natural Sciences, c. 24, sy. 1, 2023, ss. 3-9, doi:10.23902/trkjnat.1144980.
Vancouver Gazdağlı A, Albayrak G. CHARACTERIZATION OF cox3 AND rnl GENES ENCODED IN MITOCHONDRIA OF Fusarium graminearum Schwabe. Trakya Univ J Nat Sci. 2023;24(1):3-9.

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