Polygala vulgaris genome sequencing

Polygala L. (Polygalaceae) is represented by a total of 18 species, one of which is cultivated, 17 natural, and 20 taxa consisting of two subspecies in Turkiye. Polygala vulgaris L. species is rarely distributed in Marmara, Central Anatolia and Eastern Anatolia Regions in Turkiye. 2n=68, 2n=34 and 2n=28+2B chromosome numbers were determined in the population and the cytotypes of the species were defined. In this study, two populations of cytotypes were selected and this populations of P. vulgaris L. were analysed k-mer based softwares to show degree of heterozygosity using short read DNA sequences. Basic chromosome number and genome size that have been reported here are 2n=4x=68 for the first population and 2n=34; 68 for the second population. The heterozygosity levels were calculated in GenomeScope2.0 after finding the optimum number of k-mer lenghts. According to results, the heterozygosity degree in first population is average 11.22% while second population is average 6.36%.We also investigated genome sizes using several bioinformatic tools such as SGA, FindGSE, GenomeScope2.0 and Kmergenie to compare the results with the actual genome sizes obtained by flow cytometry. According to flow cytometry results the genome size was estimated 1822 Mb on average for the first population and FindGSE showed the best performance by calculating an average of 1107 Mb among these programs. For the second population, the actual genome size was 2005 Mb on average and the same program was the most succesful to estimate genome size. We present here an alternative protocol to infer ploidy level and genome size using high throghput DNA data. DNA data coming from next generation sequencing can potentially provide a useful alternative for bioinformatically estimating genome size and ploidy level. Additionally, we report flow cytometry measurements and chromosome numbers for two populations of P. vulgaris.