biostudies-literatureUnknown12(1)Wen WCyperus rotundus, one of the most aggressive weeds worldwide, demonstrates significant resistance to conventional control strategies. This species causes yield losses ranging from 20% to 90% in both agricultural and horticultural crops, posing a substantial threat to agricultural ecosystems. In this study, we present a chromosome-level genome assembly and annotation of C. rotundus. The haplotypic assembly spans approximately 293 Mb in length, with a high contig N50 of 5.49 Mb, a GC content of 36%, and a BUSCO score of 93.4%. A total of 94.03% (275.55 Mb) of the contigs were successfully mapped onto 54 chromosomes. Repetitive sequences constitute 44.78% of the genome. We predicted 23,280 protein-coding genes, 97% (52,439) of which were functionally annotated. The reference genome will serveScientific data1838https://www.ebi.ac.uk/biostudies/studies/S-EPMC12630632biostudies-literatureChromosome-Level Genome Assembly and Annotation of purple nutsedge (Cyperus rotundus Cyperaceae).PMC12630632Li TZhang YXu RFeng YChen FChen YWang HYu ZWen WfalseChromosome-Level Genome Assembly and Annotation of purple nutsedge (Cyperus rotundus Cyperaceae).Cyperus rotundus, one of the most aggressive weeds worldwide, demonstrates significant resistance to conventional control strategies. This species causes yield losses ranging from 20% to 90% in both agricultural and horticultural crops, posing a substantial threat to agricultural ecosystems. In this study, we present a chromosome-level genome assembly and annotation of C. rotundus. The haplotypic assembly spans approximately 293 Mb in length, with a high contig N50 of 5.49 Mb, a GC content of 36%, and a BUSCO score of 93.4%. A total of 94.03% (275.55 Mb) of the contigs were successfully mapped onto 54 chromosomes. Repetitive sequences constitute 44.78% of the genome. We predicted 23,280 protein-coding genes, 97% (52,439) of which were functionally annotated. The reference genome will serve2025-01-01T00:00:00Z2025 Nov2026-06-05T17:22:47.875Z2026-05-19T03:12:04.813ZS-EPMC126306324126111810.1038/s41597-025-06126-x