Sequence Analysis of the Internal Transcribed Spacer (ITS) Region of the Nuclear Ribosomal DNA (nrDNA) and Chloroplast trnL-F Region (cpDNA) of Some Lactuca L. (Asteraceae) Species in Turkey

Abstract

In the current study, sequence analysis of some Turkish Lactuca L. species using nrITS DNA and trnL-F cpDNA sequences were performed to elucidate phylogenetic relationships among the taxa under study. Hieracium umbellatum was used as an outgroup. Different plant materials of Lactuca were collected from different parts of Turkey during excursions of summer 2013. Plant materials were either kept in silica gel or kept fresh for immediate DNA isolation. Both phenol chloroform-isoamyl alcohol method and commercial kits were used to extract genomic DNA for PCR reactions. ITS4 and ITS5A primers were utilized for ITS region, while trnLe and trnLf primers were used to amplify the trnL-F region. Obtained DNA sequences were edited both manually and by using BioEdit 7.0.4.1. Sequencing data were aligned via ClustalW program and analyzed using PAUP 4.01b10 software. nrITS sequences varied from 639 nucleotides to 735 nucleotides. Average nucleotide composition for nrITS was 22.1% (T), 27.9% (C), 23.2% (A) and 26.8% (G). It was also found that divergence values differed between 0.0000 and 0.10290. The trnL-F sequences varied from 296 nucleotides to 385 nucleotides. Average nucleotide composition of trnL-F sequences was 34.1% (T), 18.4% (C), 31.6% (A) and 16.0% (G). It was also found that divergence values differed between 0.0000 and 0.09674. Neighbour Joining (NJ) trees were constructed in order to identify the relationships among Lactuca species. Phylogenetic trees based on ITS region were found to be more useful than phylogenetic trees based on trnL-F region. After analysis of the results obtained, the data suggest that Lactuca contains 2 clades, with clade 1 having 2 subclades. These results support the prior phylogenetic studies on Lactuca and hence provide an up to date review of Turkish Lactuca species.