Abstract
Cyperus difformis is a globally problematic weed in rice fields, posing a significant threat to rice yield. While chemical herbicides are commonly used for its control, the species often escapes management due to its rapid evolution of resistance to widely used herbicides. To better understand the mechanisms underlying herbicide resistance, insights into the genetics and genomics of C. difformis are essential. In this study, we present a telomere-to-telomere genome assembly of C. difformis, generated by combining PacBio HiFi, Oxford Nanopore Technologies (ONT), MGI short reads and high-throughput chromatin conformation capture (Hi-C) technologies. The assembled genome spans 226 Mb with a scaffold N50 of 13.08 Mb. Utilizing Hi-C interaction data, 97.24% of the contigs were anchored to 18 chromosomes, with 35 telomeres successfully defined. Further analysis identified 75.73 Mb of repetitive sequences and 21,069 protein-coding genes, of which 91.8% (19,347 genes) were functionally annotated. This high-quality genome provides a valuable resource for studies in population genetics, phylogeny, comparative genomics, adaptive evolution, and functional genomics of C. difformis.
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Data availability
The raw sequence data are available in the Genome Sequence Archive at https://ngdc.cncb.ac.cn/gsa/browse/CRA031324. The assembly and annotation file of Cyperus difformis are available from Figshare at https://doi.org/10.6084/m9.figshare.29072027. the assembly file is also available in NCBI at https://www.ncbi.nlm.nih.gov/nuccore/JBTANI000000000.
Code availability
All bioinformatic analyses were conducted in accordance with the respective software manuals and standard protocols. Software versions and critical parameters are reported in the Methods section, with unspecified settings retained as defaults. No custom code was developed during this study.
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Acknowledgements
This study was supported by National Natural Science Foundation of China (32360681 and 32460693), Guangxi Natural Science Foundation (2021GXNSFDA220007 and 2024GXNSFAA010013), Research Funding of Guangxi Academy of Agriculture Sciences (2021YT066, 2022JM43 and 2024ZX17), Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests (22-035-31-23ST02), Research Funding of Guangxi Vocational University of Agriculture (XKJ2305), and Guangxi Innovation Group of National Modern Agricultural Industry Technology System (nycytxgxcxtd-2024-16-03).
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Y.W. and J.L. designed this research. J.Z., W.Z. and Y.M. analyzed the data. M.Q. and W.L. collected the samples. Y.W. and J.L. drafted and revised the manuscript. All co-authors contributed to and approved this manuscript.
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Li, J., Zhao, J., Zheng, W. et al. A telomere-to-telomere genome assembly for Cyperus difformis. Sci Data (2026). https://doi.org/10.1038/s41597-026-06582-z
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DOI: https://doi.org/10.1038/s41597-026-06582-z
