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

Aylin Gazdağlı; Gülruh Albayrak

Makale detayları

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

Yazarlar:

Aylin Gazdağlı | Gülruh Albayrak

Yayıncı:

Trakya University

Ana Başlıklar:

Genetics

Dergi:

Trakya University Journal of Natural Sciences Vol.24 Issue 1, pp.3-9

Belge Tipi:

Makale

Yayın Tarihi:

4/2023

Belge Dili:

İngilizce

Document ID (Org No.):

2001287848

pISSN:

2528-9691

Anahtar kelimeler:

Özet:

 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.

 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.

 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.

 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 İrandan 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 cox3e 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, cox3e kıyasla nukleotid varyasyonlarının daha yüksek oranda taşındığı belirlendi. Kodlama bölgelerinde bulunan SNPlerin ve in-dellerin 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. Fusariumda tür içi filogenetik ilişkilerin mitokondriyal gen varyasyonuna dayalı olarak belirlenebilmesi nedeniyle yöntemin diğer mantar türlerine de uygulanabileceği önerilmektedir.

Makale detayları

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

Yazarlar:

Aylin Gazdağlı | Gülruh Albayrak

Yayıncı:

Trakya University

Ana Başlıklar:

Genetics

Dergi:

Trakya University Journal of Natural Sciences Vol.24 Issue 1, pp.3-9

Belge Tipi:

Makale

Yayın Tarihi:

4/2023

Belge Dili:

İngilizce

Document ID (Org No.):

2001287848

pISSN:

2528-9691

Fusarium graminaerum

mitochondrial genes

polymerase chain reaction (PCR)

sequencing

phylogenetic relationship

Sayı

Makale detayları

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

Yazarlar: Aylin Gazdağlı | Gülruh Albayrak

Yayıncı: Trakya University

Ana Başlıklar: Genetics

Dergi: Trakya University Journal of Natural Sciences Vol.24 Issue 1, pp.3-9

Belge Tipi: Makale

Yayın Tarihi: 4/2023

Belge Dili: İngilizce

Document ID (Org No.): 2001287848

pISSN: 2528-9691

Fusarium graminaerum

mitochondrial genes

polymerase chain reaction (PCR)

sequencing

phylogenetic relationship

Sayı

Yazarlar:

Aylin Gazdağlı | Gülruh Albayrak

Yayıncı:

Trakya University

Ana Başlıklar:

Genetics

Dergi:

Trakya University Journal of Natural Sciences Vol.24 Issue 1, pp.3-9

Belge Tipi:

Makale

Yayın Tarihi:

4/2023

Belge Dili:

İngilizce

Document ID (Org No.):

2001287848

pISSN:

2528-9691