Abstract
Cynodon species can be used for multiple purposes and have high economic and ecological significance. However, the genetic basis of the favorable agronomic traits of Cynodon species is poorly understood, partially due to the limited availability of genomic resources. In this study, we report a chromosome-scale genome assembly of a diploid Cynodon species, C. transvaalensis, obtained by combining Illumina and Nanopore sequencing, BioNano, and Hi-C. The assembly contains 282 scaffolds (~423.42 Mb, N50 = 5.37 Mb), which cover ~93.2% of the estimated genome of C. transvaalensis (~454.4 Mb). Furthermore, 90.48% of the scaffolds (~383.08 Mb) were anchored to nine pseudomolecules, of which the largest was 60.78 Mb in length. Evolutionary analysis along with transcriptome comparison provided a preliminary genomic basis for the adaptation of this species to tropical and/or subtropical climates, typically with dry summers. The genomic resources generated in this study will not only facilitate evolutionary studies of the Chloridoideae subfamily, in particular, the Cynodonteae tribe, but also facilitate functional genomic research and genetic breeding in Cynodon species for new leading turfgrass cultivars in the future.
Highlights
Bermudagrasses (Cynodon spp.) are warm-season (C4)perennial grass species that originate primarily from open areas in southeastern Africa[1]
Based on Illumina data (~18.8 Gb), k-mer frequency analysis revealed that the genome size was ~454.4 Mb (Supplementary Fig. 1), similar to the size determined by flow cytometry (~444.3 Mb) (Supplementary Fig. 2)
In order to overcome the difficulty of assembly with high levels of heterozygosity, a series of technologies, including Illumina sequencing, Nanopore sequencing, Bionano, and Hi-C, were utilized to assemble the genome, and the sequencing and assembly workflow is shown in Supplementary Fig. 3
Summary
Bermudagrasses (Cynodon spp.) are warm-season (C4)perennial grass species that originate primarily from open areas in southeastern Africa[1]. The good tolerance to abiotic stresses (i.e., traffic, heat, salinity, and drought), ability to grow in most types of soil conditions, rapid recovery potential, low growing nature and aggressive sod-forming growth habit with rhizomes and solons all make bermudagrasses the most used warm-season turfgrasses worldwide in the turf industry, and these grasses are ideally suited for any kind of application, including for ground covers, lawns, sports fields, golf course tees, fairways, and putting greens[6,10] They are important forages in the southern United States[11] and have attracted research interest as biofuel grasses[12], phytoremediation plants for soil reclamation[13,14], and medicinal plants for their pharmacognostic properties (e.g., as anti-inflammatory, diuretic, Cui et al Horticulture Research (2021)8:93 antiemetic, antidiabetic, and blood-purifying agents) in Asia and Australia[15,16]. A number of leading varieties/cultivars used for turfgrass are sterile triploid hybrids from natural (C. × magennisii) or human-made crosses between common bermudagrass and African bermudagrass, such as Tifgreen, Tifway, Tifdwrf, MS Supreme, Champion, and MiniVerde[10]
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