Fig. 1: Reference genome assemblies and phylogenomics of the Digitaria genus.

a Morphological features of the three Digitaria species: D. radicosa (#YZGJ2), D. milanjiana (#DZ2), and D. sanguinalis (#YJ2023), shown from left to right. b Genome architecture of the three Digitaria species. Track i represents the chromosomes; tracks ii-iv depict the density of annotated genes (ii), transposable elements (iii), and GC content (iv), respectively; track v illustrates syntenic relationships. C, genome of D. radicosa; D^T and E^T, subgenomes of D. milanjiana; C^H, D^H, and E^H, subgenomes of D. sanguinalis. c Phylogenetic tree constructed with single-copy orthologs using ASTRAL among Poaceae genomes. Gray nodes denote speciation events out of Digitaria, while red and blue nodes mark polyploidization and speciation events within Digitaria, respectively. Subgenome labels (e.g., A, B, C, D and E) correspond to inferred ancestral contributions in polyploids. S. viridis, Setaria viridis; E. indica, Eleusine indica; O. sativa, Oryza sativa. d Relative abundance of stress-associated gene families across Poaceae genomes. Gene family sizes were standardized as Z-scores and visualized as a gradient heatmap. Gene families associated with abiotic and biotic stress responses are indicated in blue and red, respectively. Gene families previously implicated in non-target-site herbicide resistance are highlighted in green. FAR1, Far-red impaired response 1 DNA-binding domain; Hsp70, Heat shock protein 70 family; P450, Cytochrome P450 family; ABC transporter, ATP-binding cassette transporter; GRAS, GAI-RGA- and -SCR; AP2, Apetala2; NAM C-terminal, No Apical Meristem Protein C-terminal domain; UDP/GT, UDP-glucoronosyl and UDP-glucosyl transferase; D-mannose binding lectin, D-mannose binding lectin domain; NB-ARC, nucleotide-binding adapter shared by APAF-1, R proteins, and CED-4. O. sativa, Oryza sativa; E. haploclada, Echinochloa haploclada; E. crus-galli, Echinochloa crus-galli; E. oryzicola, Echinochloa oryzicola; S. italica, Setaria italica; P. hallii, Panicum hallii; D. exilis, Digitaria exilis; D. radicosa, Digitaria radicosa; D. milanjiana, Digitaria milanjiana; D. sanguinalis, Digitaria sanguinalis. E. crus-galli A^H, B^H, and C^H, subgenomes of E. crus-galli; E. oryzicola A^T and B^T, subgenomes of E. oryzicola; D. exilis A^T and B^T, subgenomes of D. exilis; D. milanjiana D^T and E^T, subgenomes of D. milanjiana; D. sanguinalis C^H, D^H, and E^H, subgenomes of D. sanguinalis. Source data are provided as a Source Data file.