Comparison of some genes and methods used in plant molecular phylogeny

Drawing the boundaries of the classification of living organisms and living units to produce systematic knowledge based on observations and experiments with the introduction has been one of the most complex problems. For this purpose, researchers have developed many theories and methods to determine the diversity of the livings. The molecular systematic studies that reveal biodiversity have been rapidly evolving in the last 20 years. In this developing process using sequence analysis and methods of phylogenetic analysis of molecular systematic have also started to contribute the phylogenetic studies. In terms of phlogenetic information when morphological characters and fasils are insufficient for phylogenetic studies. DNA sequence analysis is very useful for phylogenetic studies. In this study, genes, gene regions, the cellular location of the gene (chloroplast, nucleus), the number of genes, which use in phylogenetic studies efficiently, four alignment programs (CLUSTAL W, T-COFFEE, MAFFT, MUSCLE), aligned data sets with these alignment methods and algorithms using common phylogenetic analysis programs were evaluated.In order to compare phylogenetic methods Distance (D), Maximum Likelihood (ML), Maximum Parsimony (MP), and Bayesian-MCMC (BI) were compared using two different data sets. Hereby, the first data set was composed of 44 cotton (Gossypium) species. This set was assessed using ITS1, ITS2, and ITS1-ITS2 DNA sequences of nuclear ribosomal RNA. The second set composed of 60 taxa containing shrubs, woody, herbaceous, monocotyledon and dicoytledon were evaluated using 5 different chloroplast genes (matK, trnH-psbA, accD, rpoC1, rpoB).The consequence of this study, based on our analysis, MAFFT alignment software aligned our data the best fit and had gave the right tree topology for Gossypium species. At the same time the most appropriate subtitüsyon models were GTR and TN93 for the current data. Based on the bootstrap and posterior probability values matK and trnH-psbA genes were determined as the marker genes for the sixty plant taxa used in the study.KEYWORDS: Phylogeny, molecular systematic, bioinformatic, phylogeny analysis