A whole-genome assembly of St. Augustinegrass and visualizing diversity within the species

St. Augustinegrass [Stenotaphrum secundatum (Walt.) Kuntze] is a warm-season turfgrass species in the family Poaceae. This species is a popular choice for lawns in the Southern United States, due to its higher tolerance to shade, heat and humidity. However, there is little genomic information available to researchers and breeders, limiting knowledge on the genetic basis for favorable traits. We present a reference-grade chromosome-scale genome assembly for the popular freeze-tolerant diploid cultivar Raleigh. The reference genome has been resolved into two haplotype assemblies (465.41 and 401.52 Mb), accounting for 95.2% and 82.1% of the expected haplotype genome size respectively, each anchored on the nine chromosomes and a total of 62,454 genes. Analysis of the assembly revealed 50.70% of the genome contained repeats. Analysis of the diversity within the species was investigated across 79 genotypes including commercial cultivars, breeding lines, and plant introductions by low-coverage sequencing identifying 605,038 single nucleotide polymorphisms (SNPs). The SNPs were used to investigate genetic diversity across the panel and the effectiveness of low-coverage sequencing on the high GC content species. SNPs classified genotypes into groups matching their phylogenetic and breeding history, with the plant introductions clustering into two groups on either side of the plot. Breeding lines for those whose parents existed in the panel clustered in between the two parents. These results showed that the cheaper, low-coverage option can be used for this type of analysis. Together, all of the resources produced in this study allow the start of the genomics-enabled genetic improvement for St. Augustinegrass.