Primer Design for matK Sequences of the Quercus L. Species

The genus Quercus L. distributed in wide geographical regions and that is representing a significant portions of forest ecosystems in this geographical regions is taxonomically very problematic. Weak reproductive barriers between species especially classified within same section increase the hybridization and finally it makes problematic the genus. Moreover, variations in the species exposed to different climatic and geographical conditions, in addition to lack of adequate conservation programs and destructions of many species because of their high economic values is another important reason to increase the problems in the genus. MatK sequences belonging to cpDNA is one of the most frequently used regions in DNA barcoding studies to determine the problematic taxa and evaluate their phylogenetic relationships. However, the primers designed for the amplification of matK sequences are stated by universal. In other words, they have not been specifically designed by examination of sequences belonging to oak species and they cannot generally synthesize the all matK sequences. In this study, eleven primer pairs were designed to synthese the complete matK sequences of Quercus species and their sequence compatibilities were evaluated in different species of the genus. Furthermore, seconder structure tendencies of all primer pairs such as homodimer, heterodimer and hairpin, besides their nucleotide lengths, melting temperatures and GC contents were examined in detailed. The sequences containing the trnK introns located on both sides of matK region, in addition to matK sequencesto amplify the complete matK sequences in PCR were prefered to design the primers. Here, the initial and final sequences of the matK region for Quercus species were determined and it is also analyzed how many nucleotides were synthesized from outside the matK sequences with each designed primer pairs.