Polygala vulgaris L. (Polygalaceae)'in Ploidi Düzeyinin Yeni Nesil Dizileme Yöntemiyle İncelenmesi

Abstract

In this thesis study, the whole genome sequencing of five individuals from two different populations of the tetraploid species Polygala vulgaris L., with a chromosome number of 2n=4x=68, was analyzed using bioinformatics tools. Genome size estimation methods, including k-mer based and non-k-mer based programs, were utilized and their results were compared. Additionally, genome heterozygosity estimation, the classification of transposable elements, and their relationships with polyploidy were investigated, and the findings were discussed. Furthermore, through polyploid genome analyses, the polyploidy events each individual experienced during their evolutionary history, the timing of these events, and duplication types other than whole-genome duplication were also estimated. The whole genome sequences of the taxa were mapped using the de novo assembly method. In the five studied individuals, genome sizes were estimated to range between 1300–2024 Mb with Kmergenie (k-mer based), 68–404 Mb with GenomeScope, and 1224–1951 Mb with the non-k-mer based SGA program. Heterozygosity levels were calculated as 4.8%, 16%, 21.68%, 10%, and 4.56%. The transposable element contents in each genome were found to be 49.39%, 45.62%, 43.16%, 51.01%, and 45.15%, indicating that nearly half of the genome content consists of transposons. Bioinformatics analyses revealed that the emergence of the species occurred approximately 65–72 million years ago (mya) and that both populations experienced two paleo-polyploidy events. The first polyploidy event was estimated to have occurred around 55 million years ago, while the second occurred approximately 34 million years ago. As a result of this study, it was demonstrated that information such as ploidy detection and genome size, traditionally obtained through classical methods and laboratory conditions, can also be derived through bioinformatic analyses. This minimizes the margin of error in laboratory conditions and enables access to much more information and analyses using the available sequence data. Through this thesis, the first whole-genome sequence of Polygala vulgaris individuals was obtained, the timing of ploidy events was estimated, and the emergence time of the species was determined. Moreover, the first genome characterization of this species was conducted by analyzing short reads obtained through next-generation sequencing.