The telomere-to-telomere genome of Cyperus rotundus L. provides new insights into the molecular mechanisms of herbicide resistance and α-cyperone biosynthesis

文献类型： 外文期刊

第一作者： Luo, Yongjian

作者： Luo, Yongjian;Wang, Yiqiang;Luo, Yongjian;Wang, Ru;Zhang, Yixin;Liu, Jun;Luo, Yongjian;Wang, Yiqiang;Luo, Yongjian;Wang, Yiqiang

作者机构：

关键词： Weed control; Telomere-to-telomere genome; Cyperone; Whole-genome duplication; Chromosomal evolution

期刊名称：INDUSTRIAL CROPS AND PRODUCTS （ 影响因子：6.2； 五年影响因子：6.2 ）

ISSN： 0926-6690

年卷期： 2025 年 233 卷

页码：

收录情况： SCI

摘要： Cyperus rotundus L. (purple nutsedge) is an invasive weed with medicinal value, but its genomic resources are limited, hindering research on bioactive compound biosynthesis and herbicide resistance mechanisms. This study presents the first telomere-to-telomere (T2T) genome assembly of C. rotundus, generated using Illumina, PacBio, and Hi-C technologies. The genome consists of 55 pseudochromosomes (285.57 Mb, N50 = 5.64 Mb), with 58.31% repetitive sequences and 25,289 protein-coding genes. Phylogenetic analysis indicates that C. rotundus diverged from Cyperus esculentus around 4.75 million years ago and experienced a whole genome duplication (WGD) event approximately 5.4 MYA. Chromosomal evolution analysis revealed fusion and fission events, offering insights into karyotype evolution in the Cyperaceae family. Integrated transcriptomic and metabolomic analyses identified sesquiterpenoids and monoterpenoids as primary terpenoid classes, with higher accumulation in tubers and roots. We predicted CroTPS11-14 as a key enzyme in cyperone precursor biosynthesis and identified 10 transcription factors potentially regulating sesquiterpenoid biosynthesis. Additionally, multiple herbicide target genes were found to have multiple copies, such as acetyl-CoA carboxylase (ACCase), acetolactate synthase (ALS), phytoene desaturase (PDS), and protoporphyrinogen oxidase (PPO). Gene family expansion analysis revealed a large number of non-target resistance genes and adaptive genes related to flooding stress, such as superoxide dismutase (SOD), Flavoprotein oxidoreductases (FMN), Glycosyltransferases (GT1), Calcium-dependent protein kinase (CPK15), sucrose synthase (SUS1), and LRR receptor-like kinases. Further in vitro enzyme activity assays and q-PCR revealed that these genes may play roles in herbicide resistance and environmental adaptability. This research offers a high-quality genomic resource for C. rotundus, shedding light on its medicinal compound biosynthesis and herbicide resistance mechanisms, and providing valuable insights for molecular breeding, medicinal development, and sustainable weed control strategies.

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