A High-Quality Haplotype-Resolved Genome of Common Bermudagrass (Cynodon dactylon L.) Provides Insights Into Polyploid Genome Stability and Prostrate Growth

Abstract

Common bermudagrass (Cynodon dactylon L.) is an important perennial warm-season turfgrass species with great economic value. However, the reference genome is still deficient in C. dactylon, which severely impedes basic studies and breeding studies. In this study, a high-quality haplotype-resolved genome of C. dactylon cultivar Yangjiang was successfully assembled using a combination of multiple sequencing strategies. The assembled genome is approximately 1.01 Gb in size and is comprised of 36 pseudo chromosomes belonging to four haplotypes. In total, 76,879 protein-coding genes and 529,092 repeat sequences were annotated in the assembled genome. Evolution analysis indicated that C. dactylon underwent two rounds of whole-genome duplication events, whereas syntenic and transcriptome analysis revealed that global subgenome dominance was absent among the four haplotypes. Genome-wide gene family analyses further indicated that homologous recombination-regulating genes and tiller-angle-regulating genes all showed an adaptive evolution in C. dactylon, providing insights into genome-scale regulation of polyploid genome stability and prostrate growth. These results not only facilitate a better understanding of the complex genome composition and unique plant architectural characteristics of common bermudagrass, but also offer a valuable resource for comparative genome analyses of turfgrasses and other plant species.

Whole‐genome sequencing of allotetraploid bermudagrass reveals the origin of Cynodon and candidate genes for salt tolerance

“…Further analysis revealed that 97.5% of Illumina short reads were mapped to our genome assembly, with a base-level accuracy of 99.5%. At the whole-genome level, BUSCO (Sim O et al, 2015) evaluation revealed that 97.3% of the set consisted of 1614 complete BUSCO genes (Table 1; Table S4), which is similar to the percentages reported in C. transvaalensis (2n = 2x = 18) (Cui et al, 2021) and Yangjiang (C. dactylon 'Yangjiang') (Zhang et al, 2022), implying that our bermudagrass assembly is complete. The assembly's completeness and contiguity were also verified using the LTR assembly index (LAI) .…”

Recent Advances in Assembly of Complex Plant Genomes

“…Here, to explore effectual phased tools and strategies for assembling complex plant genomes, we have summarized the recently published haplotype-resolved assemblies in plant genomes. We have further divided these assembly approaches into two strategies: reference-based variant phasing and de novo assembly-based haplotype phasing ( Table 1 ) [12] , [51] , [14] , [15] , [16] , [17] , [18] , [61] , [62] , [63] , [64] , [65] , [66] , [67] , [68] , [69] , [70] , [71] , [72] , [73] , [74] , [75] , [76] , [77] , [78] , [79] , [80] , [81] , [82] , [83] , [84] , [85] , [86] , [87] , [88] , [89] , [90] .…”

Bioassay of Allelopathic Potential of Bermudagrass and Sorghum on Germination and Related Traits of Weeds Associated With Rice

“…Bermudagrass contains many allelochemicals such as Caffeic, Ferulic, P-Coumaric, P-Hydroxybenzoic Syringic Acids and Vanillic (Mahmoodzadeh, 2010). These phenolics represent the effect of allelopathy which supports the statement that phytotoxicity of bermudagrass may be because of the occurrence of phenolic compounds (Zhang et al, 2022). Experiments under laboratory are thought to be indispensable and useful to investigate the allelopathic potential of any plant (Tibugari et al, 2020).…”

“…Bermudagrass (Cynodon dactylon L.) is well known as worst weed that is found almost everywhere in the world and it consists of the fourth most allelopathic compounds (Zhang et al, 2022). Due to its compatibility for water, nutrients, space and the soil oxygen, bermudagrass is often an effective colonizer (Chen et al, 2021).…”