Phylogenetic analysis of some Citrus L. (Rutaceae) taxa in Turkey based on chloroplast (cPDNA) trnL intron and trnL-F DNA sequences

In this study, phylogenetic analysis of some Turkish Citrus species was conducted based on chloroplast DNA (trnL intron and trnL-F) sequences. Citrus taxa were plotted on a phylogenetic tree where Zanthoxylum ailanthoides was used as the outgroup. The sequences for trnL intron and trnL-F regions of the outgroup were retrieved from NCBI GenBank. All plant samples were collected from different locations during the inflorescence and vegetation periods, and brought to the laboratory. Genomic DNA was isolated from healthy green leaves using DNAeasy Plant Mini Kit. trnL intron region was amplified using universal primers trnc and trnd, while for the trnL-F region trne and trnf were used. Later obtained DNA sequences were edited using BioEdit 7.0.4.1 and FinchTV. Sequencing data were aligned via ClustalW program and analyzed using MEGA 6.0 software. Maximum Likelihood and bootstrap trees were constructed in order to identify the relationships among Citrus taxa. The trnL intron sequences ranged from 554 to 581 nucleotides. The average nucleotide composition of trnL intron was 26.3% T, 16.8% C, 37.7% A and 19.2% G. The divergence values varied from 0.000 to 0.057. The trnL-F sequences ranged from 392 to 399 nucleotides. Average nucleotide composition was 34.3% T, 21.2% C, 27.4% A and 17.1% G, while the divergence values of trnL-F sequences varied from 0.000 to 0.003. As a result, trees constructed based on trnL intron region have systematically been found to show more reliable and compatible results than those formed based on the trnL-F region