Survey sequencing and flow cytometry reveal the genomic characteristics and genetic markers of six wild sweetpotato species.

Abstract

Background: The lack of genomic and genetic research on wild sweetpotato species has hindered the advancement of sweetpotato variety development through modern crop improvement techniques.

Methods and results: To facilitate the use of genomic and genetic approaches in sweetpotato variety development, we conducted a comprehensive assessment of the genome size and ploidy of six closely related wild sweetpotato species using flow cytometry and chromosome counting. Additionally, we acquired insights into their genomic characteristics through high-throughput sequencing. Based on the 17-mer frequency distribution, the genome sizes of these species ranged from 518.47 Mb to 1,505.04 Mb. Notably, most diploid species exhibited genome sizes of approximately 500 Mb, with the diploid wild species I. purpurea standing out as having a significantly larger genome size compared to other diploid species. A substantial proportion of repeats (ranging from 57.47 to 81.07%) was identified across the genomes of the six species. Heterozygosity levels varied from 0.24 to 2.21%. SSR analysis revealed that the distribution of microsatellite patterns was largely consistent among the genomes of I I. lacunosa, I. tenuissima, and I. tiliacea, with mono-, di-, and trinucleotide motifs dominated by A/T, AT/AT, and AAT/ATT, respectively, indicating a strong A/T base preference. SNPs in this study were unevenly distributed across chromosomes, and non-synonymous SNVs in exonic accounted for 3.199% of the total number of SNPs, which may lead to genetic functional variation between species. In addition, the cross-regional annotation of SNPs highlights the diversity of gene regulatory regions and may provide insights into gene regulation, the underlying genetics of complex traits, and genetic differences between species.

Conclusion: The current data reinforce the established positive correlation between genome size and ploidy in the genus Ipomoea. In particular, the diploid I. purpurea had a larger genome compared to other diploid species. The genome survey indicated that I. lacunosa(2x), I. tiliacea(2x), and I. tenuissima(2x) possess simple genomes with low heterozygosity (0.36%, 0.37%, and 0.24%, respectively). In contrast, I. purpurea(2x) has a simple genome but exhibits high heterozygosity (1.95%), while I. tabascana(4x) and I. trifida(6x) have complex genomes with high heterozygosity (2.21% and 1.54%, respectively). These results provide a reasonable basis for the selection of whole genome sequencing strategies for these species and would provide references for research into the genetic diversity of wild relatives of sweetpotato.