Sequence Analysis and Genetic Diversity of ndhF of the Chloroplast DNA (cpDNA) of Chrysophthalmum (Asteraceae) Species in Türkiye

Absract: In this study, chloroplast DNA (cpDNA) ndhF sequence analysis was used to determine the sequence analysis and genetic diversity of Chrysophthalmum Schultz Bip. species distributed in Türkiye. Genomic DNA was isolated from green leaves and cpDNA ndhF region was amplified by PCR. The results of the PCR, the forward and reverse sequences were edited using the Sequencher 5.4.6 programme and the contig sequences were obtained. To determine the phylogenetic relationships between species, MEGA 6.0 was used to construct a maximum likelihood (ML) tree. Using the same program, nucleotide composition, phylogenetic trees, genetic distance matrix, and genetic diversity analyses were performed. In addition, the physicochemical properties and 3D structure of ndhF proteins were determined. From the results of the ndhF analyses, the nucleotide length of Chrysophthalmum species was found to vary between 471 and 625. The genetic matrix value was determined to be between 0.000 and 0.009. In the phylogenetic tree constructed using ndhF sequences from Anvillea DC., Pulicaria Gaertn., Limbarda Adans, Inula L., Carpesium L., Pentanema Cass., Dittrichia Greuter, Rhanteriopsis Rauschert and Telekia Baumg species from NCBI, C. montanum was grouped with Inula, Pentanema and Rhanteriopsis species. C. gueneri was grouped with C. dichotomum and Pentanema alanyense. Previous phylogenetic studies were in agreement with our results. In addition, the ndhF results supported that Chrysophthalmum species are not a monophyletic group.