Chromosome-scale Genome Assembly of the Yellow Nutsedge (Cyperus esculentus)

文献类型： 外文期刊

第一作者： Zhao, Xiaoqing

作者： Zhao, Xiaoqing;Ren, Yongfeng;Hou, Zhihui;Su, Shaofeng;Wang, Jianguo;Cheng, Yuchen;Lu, Zhanyuan;Zhao, Xiaoqing;Ren, Yongfeng;Li, Juan;Dong, Qi;Lu, Zhanyuan;Zhao, Xiaoqing;Ren, Yongfeng;Cheng, Yuchen;Lu, Zhanyuan;Zhao, Xiaoqing;Cheng, Yuchen;Lu, Zhanyuan;Yi, Liuxi;Ren, Wei;Zhang, Yuanyu;Yang, Xiangdong

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关键词： chromosome-scale genome; Cyperus esculentus; yellow nutsedge; oil plant

期刊名称：GENOME BIOLOGY AND EVOLUTION （ 影响因子：3.3； 五年影响因子：3.5 ）

ISSN： 1759-6653

年卷期： 2023 年 15 卷 3 期

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收录情况： SCI

摘要： The yellow nutsedge (Cyperus esculentus L. 1753) is an unconventional oil plant with oil-rich tubers, and a potential alternative for traditional oil crops. Here, we reported the first high-quality and chromosome-level genome assembly of the yellow nutsedge generated by combining PacBio HiFi long reads, Novaseq short reads, and Hi-C data. The final genome size is 225.6 Mb with an N50 of 4.3 Mb. More than 222.9 Mb scaffolds were anchored to 54 pseudochromosomes with a BUSCO score of 96.0%. We identified 76.5 Mb (33.9%) repetitive sequences across the genome. A total of 23,613 protein-coding genes were predicted in this genome, of which 22,847 (96.8%) were functionally annotated. A whole-genome duplication event was found after the divergence of Carex littledalei and Rhynchospora breviuscula, indicating the rich genetic resources of this species for adaptive evolution. Several significantly enriched GO terms were related to invasiveness of the yellow nutsedge, which may explain its plastic adaptability. In addition, several enriched Kyoto Encyclopedia of Genes and Genomes pathways and expanded gene families were closely related with substances in tubers, partially explaining the genomic basis of characteristics of this oil-rich tuber.

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