Fatih Coşkun, Emre Sevindik, Halil Güngör, Hasan Özçelik Balıkesir Üniversitesi Fen-Edebiyat Fakü... more Fatih Coşkun, Emre Sevindik, Halil Güngör, Hasan Özçelik Balıkesir Üniversitesi Fen-Edebiyat Fakültesi, Biyoloji Bölümü, Çağış Kampüsü, 10145 Balıkesir, ph.d-emre@hotmail.com Balıkesir Üniversitesi Fen Bilimleri Enstitüsü, Biyoloji ABD, Çağış Kampüsü, Balıkesir Muğla Üniversitesi Fen Fakültesi, Biyoloji Bölümü, Kötekli, Muğla Süleyman Demirel Üniversitesi Fen-Edebiyat Fakültesi, Biyoloji Bölümü, Isparta
In this study, genomic DNA isolation methods on six taxa belonging to two different sections of t... more In this study, genomic DNA isolation methods on six taxa belonging to two different sections of the aromatic plant genus Silene L. (Caryophyllaceae) were investigated. The gDNA isolation methods were investigated on two taxa from the section Brachypodeae Boiss. (S. leptoclada Boiss. and Silene balansae Boiss.) and four taxafrom the section Auriculatae Boiss. (S. araratica Schischk.subsp. araratica, S. lucida Chowdh.subsp. lucida, S. oligotricha Hub.-Mor. and S. caucasica(Bunge)Boiss.). During the study, Phenol-chloroform-isoamyl alcohol isolation procedure and Sigma DNA isolation commercial kit protocol were used. Purity and the amount of obtained gDNAs were determined via gel electrophoresis and spectrophotometry (A260/A280). Based on the results of the taxa studied, Phenolchloroform-isoamyl alcohol isolation procedure was found as the method yielding the highest amount of the DNA as ng in 1 stock.
DNA markers based on the PCR techniques are being broadly utilized during the past two decades. R... more DNA markers based on the PCR techniques are being broadly utilized during the past two decades. Randomly Amplified Polymorphic DNA (RAPD) is one of these techniques employed for determining the polymorphisms. In this study, we performed a molecular analysis using DNA markers for some olive (Olea europaea) cultivars grown in the Marmara Region of Turkey. Our goal was to determine the genetic relationships between 12 olive cultivars and ‘Delice’, the outgroup. Seven RAPD primers out of 60 (10 base-pair long) amplified gDNAs with repeatable bands. These primers generated 84 characters / bands in total and 39 out of these were polymorphic. After a Branch-and-Bound analysis and a Neighbour Joining (NJ) analysis via PAUP* software, the smallest genetic distance was found between Gordales and Karamursel Su cultivars as 0.03571 whereas the greatest distances were found between Arbequina and Ascolana, Manzanilla, Hermandos, Gemlik, Verdial and Vegral cultivars as 0.17857, respectively. Maxim...
As a member of the large family Fabaceae, red buds are widely cultivated in the world due to thei... more As a member of the large family Fabaceae, red buds are widely cultivated in the world due to their ornamental value. This study included 13 Cercis taxa from different parts of the world. Our analysis of the ITS nrDNA sequences proved useful in understanding the phylogenetic relationships of Cercis taxa and resolved most of the branches in the phylogenetic tree. The lowest sequence divergence within ingroup taxa was between C. canadensis ssp. canadensis and C. californica ssp. californica, 0.0014%. This was assuring that these taxa belong to the same species. The highest sequence divergence within ingroup taxa was 0.028% between C. canadensis ssp. mexicana and C. chingii. ITS data indicated that C. chuniana and C. occidentalis are interestingly close relatives, on one hand and C. siliquastrum and other North American Cercis taxa along with C.griffithii are close relatives on the other.
Yaygin bir bahce bitkisi olarak yetistirilen erguvan, Cercis, cinsinin Kuzey Amerika’da, Cin’de, ... more Yaygin bir bahce bitkisi olarak yetistirilen erguvan, Cercis, cinsinin Kuzey Amerika’da, Cin’de, ve Avrasya’da yaygin olan turleri uzerinde bitkilerin ITS ribozomal cekirdek DNA’larinin organik baz dizileri kullanilarak, filogenetik sistematik analizi yapilmistir. ITS marker’inin analizi sonucunda beklenilenden farkli olarak Avrasya’da yaygin olan erguvan ile Kuzey Amerika’daki erguvan turleri arasinda cok yakin bir akrabalik oldugu bulunmustur. Diger taraftan Cin erguvaninin ise Avrasya erguvanina yakin olmasi beklenirken daha uzak bir akraba oldugu belirlenmistir. Ayrica bu calismanin verileri Kuzey Amerika’daki yabani erguvan bitkilerinin ayni turun (Cercis canadensis) varyeteleri oldugu yonundeki hipotezi desteklemektedir
Simple, fast, low-cost and high throughput protocols are required for DNA isolation of plant spec... more Simple, fast, low-cost and high throughput protocols are required for DNA isolation of plant species. In this study, phenol chloroform isoamyl alcohol and commercial (Sigma) DNA isolation kit methods were applied on some Inula species that belong to Asteraceae family. Genomic DNA amounts, A260, A280, A260/A230 and purity degrees (A260/A280) that were obtained through both methods were measured through electrophoresis and spectrophotometer. Additionally, PCR amplification was realized by primer pairs specific to nrDNA ITS, cpDNA ndhF (972F-1603R) and trnL-F regions. Results showed that maximum genomic DNA in nanograms obtained by phenol chloroform isoamyl alcohol method. The study also revealed that I. macrocephala had the maximum DNA and I. heterolepis had the minimum DNA amount. A260/A280 purity degrees showed that the highest and lowest purity in gDNAs obtained through phenol-choloform isoamyl alcohol method were in I.aucheriana and I. salicina, respectively. The highest and lowes...
Fatih Coşkun, Emre Sevindik, Halil Güngör, Hasan Özçelik Balıkesir Üniversitesi Fen-Edebiyat Fakü... more Fatih Coşkun, Emre Sevindik, Halil Güngör, Hasan Özçelik Balıkesir Üniversitesi Fen-Edebiyat Fakültesi, Biyoloji Bölümü, Çağış Kampüsü, 10145 Balıkesir, ph.d-emre@hotmail.com Balıkesir Üniversitesi Fen Bilimleri Enstitüsü, Biyoloji ABD, Çağış Kampüsü, Balıkesir Muğla Üniversitesi Fen Fakültesi, Biyoloji Bölümü, Kötekli, Muğla Süleyman Demirel Üniversitesi Fen-Edebiyat Fakültesi, Biyoloji Bölümü, Isparta
In this study, genomic DNA isolation methods on six taxa belonging to two different sections of t... more In this study, genomic DNA isolation methods on six taxa belonging to two different sections of the aromatic plant genus Silene L. (Caryophyllaceae) were investigated. The gDNA isolation methods were investigated on two taxa from the section Brachypodeae Boiss. (S. leptoclada Boiss. and Silene balansae Boiss.) and four taxafrom the section Auriculatae Boiss. (S. araratica Schischk.subsp. araratica, S. lucida Chowdh.subsp. lucida, S. oligotricha Hub.-Mor. and S. caucasica(Bunge)Boiss.). During the study, Phenol-chloroform-isoamyl alcohol isolation procedure and Sigma DNA isolation commercial kit protocol were used. Purity and the amount of obtained gDNAs were determined via gel electrophoresis and spectrophotometry (A260/A280). Based on the results of the taxa studied, Phenolchloroform-isoamyl alcohol isolation procedure was found as the method yielding the highest amount of the DNA as ng in 1 stock.
DNA markers based on the PCR techniques are being broadly utilized during the past two decades. R... more DNA markers based on the PCR techniques are being broadly utilized during the past two decades. Randomly Amplified Polymorphic DNA (RAPD) is one of these techniques employed for determining the polymorphisms. In this study, we performed a molecular analysis using DNA markers for some olive (Olea europaea) cultivars grown in the Marmara Region of Turkey. Our goal was to determine the genetic relationships between 12 olive cultivars and ‘Delice’, the outgroup. Seven RAPD primers out of 60 (10 base-pair long) amplified gDNAs with repeatable bands. These primers generated 84 characters / bands in total and 39 out of these were polymorphic. After a Branch-and-Bound analysis and a Neighbour Joining (NJ) analysis via PAUP* software, the smallest genetic distance was found between Gordales and Karamursel Su cultivars as 0.03571 whereas the greatest distances were found between Arbequina and Ascolana, Manzanilla, Hermandos, Gemlik, Verdial and Vegral cultivars as 0.17857, respectively. Maxim...
As a member of the large family Fabaceae, red buds are widely cultivated in the world due to thei... more As a member of the large family Fabaceae, red buds are widely cultivated in the world due to their ornamental value. This study included 13 Cercis taxa from different parts of the world. Our analysis of the ITS nrDNA sequences proved useful in understanding the phylogenetic relationships of Cercis taxa and resolved most of the branches in the phylogenetic tree. The lowest sequence divergence within ingroup taxa was between C. canadensis ssp. canadensis and C. californica ssp. californica, 0.0014%. This was assuring that these taxa belong to the same species. The highest sequence divergence within ingroup taxa was 0.028% between C. canadensis ssp. mexicana and C. chingii. ITS data indicated that C. chuniana and C. occidentalis are interestingly close relatives, on one hand and C. siliquastrum and other North American Cercis taxa along with C.griffithii are close relatives on the other.
Yaygin bir bahce bitkisi olarak yetistirilen erguvan, Cercis, cinsinin Kuzey Amerika’da, Cin’de, ... more Yaygin bir bahce bitkisi olarak yetistirilen erguvan, Cercis, cinsinin Kuzey Amerika’da, Cin’de, ve Avrasya’da yaygin olan turleri uzerinde bitkilerin ITS ribozomal cekirdek DNA’larinin organik baz dizileri kullanilarak, filogenetik sistematik analizi yapilmistir. ITS marker’inin analizi sonucunda beklenilenden farkli olarak Avrasya’da yaygin olan erguvan ile Kuzey Amerika’daki erguvan turleri arasinda cok yakin bir akrabalik oldugu bulunmustur. Diger taraftan Cin erguvaninin ise Avrasya erguvanina yakin olmasi beklenirken daha uzak bir akraba oldugu belirlenmistir. Ayrica bu calismanin verileri Kuzey Amerika’daki yabani erguvan bitkilerinin ayni turun (Cercis canadensis) varyeteleri oldugu yonundeki hipotezi desteklemektedir
Simple, fast, low-cost and high throughput protocols are required for DNA isolation of plant spec... more Simple, fast, low-cost and high throughput protocols are required for DNA isolation of plant species. In this study, phenol chloroform isoamyl alcohol and commercial (Sigma) DNA isolation kit methods were applied on some Inula species that belong to Asteraceae family. Genomic DNA amounts, A260, A280, A260/A230 and purity degrees (A260/A280) that were obtained through both methods were measured through electrophoresis and spectrophotometer. Additionally, PCR amplification was realized by primer pairs specific to nrDNA ITS, cpDNA ndhF (972F-1603R) and trnL-F regions. Results showed that maximum genomic DNA in nanograms obtained by phenol chloroform isoamyl alcohol method. The study also revealed that I. macrocephala had the maximum DNA and I. heterolepis had the minimum DNA amount. A260/A280 purity degrees showed that the highest and lowest purity in gDNAs obtained through phenol-choloform isoamyl alcohol method were in I.aucheriana and I. salicina, respectively. The highest and lowes...
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