Estimation of Genome Size in the Endemic Species Reseda pentagyna and the Locally Rare Species Reseda lutea Using comparative Analyses of Flow Cytometry and K-Mer Approaches

Abstract

Genome size is one of the fundamental cytogenetic features of a species, which is critical for the design and initiation of any genome sequencing projects and can provide essential insights in studying taxonomy, cytogenetics, phylogenesis, and evolutionary studies. However, this key cytogenetic information is almost lacking in the endemic species Reseda pentagyna and the locally rare species Reseda lutea in Saudi Arabia. Therefore, genome size was analyzed by propidium iodide PI flow cytometry and compared to k-mer analysis methods. The standard method for genome size measures (flow cytometry) estimated the genome size of R. lutea and R. pentagyna with nuclei isolation MB01 buffer were found to be 1.91 ± 0.02 and 2.09 ± 0.03 pg/2 °C, respectively, which corresponded approximately to a haploid genome size of 934 and 1.022 Mbp, respectively. For validation, K-mer analysis was performed on both species’ Illumina paired-end sequencing data from both species. Five k-mer analysis approaches were examined for biocomputational estimation of genome size: A general formula and four well-known programs (CovEST, Kmergenie, FindGSE, and GenomeScope). The parameter preferences had a significant impact on GenomeScope and Kmergenie estimates. While the general formula estimations did not differ considerably, with an average genome size of 867.7 and 896. Mbp. The differences across flow cytometry and biocomputational predictions may be due to the high repeat content, particularly long repetitive regions in both genomes, 71% and 57%, which interfered with k-mer analysis. GenomeScope allowed quantification of high heterozygosity levels (1.04 and 1.37%) of R. lutea and R. pentagyna genomes, respectively. Based on our observations, R. lutea may have a tetraploid genome or higher. Our results revealed fundamental cytogenetic information for R. lutea and R. pentagyna, which should be used in future taxonomic studies and whole-genome sequencing.