Evaluation of Phylogenetic Relationships by Using psbA-trnH IGS Region of Chloroplast DNA in the Species of the Genus Quercus L.

Abstract

The psbA-trnH IGS region belonging to chloroplast genome is one of the regions which most frequently used in plants for barcoding because of it’s nucleotide sequence differences. For this purpose, this region was chosen in this study in order to contribute to the solution of taxonomic problems in oaks and to evaluate phylogenetic relationships between species. Firstly, the sequence information of the psbA-trnH IGS region was obtained from NCBI for analysis. Then, these sequences were aligned and analysis for variable sites such as substitution from one base to another base, transition / transversion ratios, and base frequencies were performed using the MEGA X program. Finally, Neighbor-joining dendrogram was prepared and analyzed in order to evaluate the phylogenetic relationships between the species. Although this region has sufficient variation for sectional separation of oak species, sequence variations were found to be insufficient in species separation and identification. As a result of the study, it is suggested that the psbA-trnH IGS sequence alone is insufficient for barcoding in oaks, however it will be beneficial to use it with different barcoding regions together.

Keywords

• psbA-trnH IGS,NCBI,MEGA X,Transition/transversion,Neighbor-joining dendrogram,Barcoding

Quercus L. Cinsine Ait Türlerde Kloroplast DNA’ya Ait psbA-trnH IGS Bölgesinin Kullanılarak Filogenetik İlişkilerin Değerlendirilmesi

Abstract

Kloroplast genoma ait psbA-trnH IGS bölgesi, en fazla nükleotid dizi farklılığı içeren bölgelerden biri olmasından dolayı barkodlama amacı ile bitkilerde sıklıkla kullanılan bölgelerden biridir. Bu amaçla meşelerde var olan taksonomik problemlerin çözümüne katkı sağlamak ve türler arasındaki filogenetik ilişkileri değerlendirmek adına bu bölge bu çalışmada tercih edilmiştir. İlk olarak psbA-trnH IGS bölgesine ait sekans bilgisi analizler için NCBI’den sağlanılmıştır. Daha sonra bu sekanslar hizalandırılmış ve varyasyon gösteren bölgeler için bir bazın diğerine değişim oranları, transisyon/transversiyon oranları, baz frekansları gibi analizler MEGA X programı kullanılarak yapılmıştır. Son olarak, türlerin birbirleri ile olan filogenetik ilişkilerini değerlendirmek adına Neighbor-joining dendrogram hazırlanmış ve analiz edilmiştir. Bu bölgenin meşe türlerinin seksiyonel ayrımı için yeterli varyasyona sahip olmasına karşın, tür ayrımında ve tanımlamasında sekans varyasyonlarının yetersiz kaldığı görülmüştür. Çalışmanın sonucu olarak psbA-trnH IGS sekansının meşelerde barkodlama amacı ile tek başına yetersiz olduğu, bununla birlikte farklı barkodlama bölgeleri ile kullanımının fayda sağlayacağı önerilmektedir.

Keywords

• psbA-trnH IGS,NCBI,MEGA X,Transisyon/transversiyon,Neighbor-joining dendrogram,Barkodlama

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