Chromosome-scale genome assembly of Cucumis hystrix-a wild species interspecifically cross-compatible with cultivated cucumber

文献类型： 外文期刊

第一作者： Qin, Xiaodong

作者： Qin, Xiaodong;Lou, Qunfeng;Xia, Lei;Li, Ji;Li, Mengxue;Zhao, Xiaokun;Yang, Shuqiong;Yu, Xiaqing;Cheng, Chunyan;Chen, Jinfeng;Zhang, Zhonghua;Zhang, Zhonghua;Xu, Yuanchao;Li, Qing;Zhou, Junguo;Huang, Sanwen

作者机构：

期刊名称：HORTICULTURE RESEARCH （ 影响因子：6.793； 五年影响因子：6.589 ）

ISSN： 2662-6810

年卷期： 2021 年 8 卷 1 期

页码：

收录情况： SCI

摘要： Cucumis hystrix Chakr. (2n=2x=24) is a wild species that can hybridize with cultivated cucumber (C. sativus L., 2n=2x=14), a globally important vegetable crop. However, cucumber breeding is hindered by its narrow genetic base. Therefore, introgression from C. hystrix has been anticipated to bring a breakthrough in cucumber improvement. Here, we report the chromosome-scale assembly of C. hystrix genome (289Mb). Scaffold N50 reached 14.1Mb. Over 90% of the sequences were anchored onto 12 chromosomes. A total of 23,864 genes were annotated using a hybrid method. Further, we conducted a comprehensive comparative genomic analysis of cucumber, C. hystrix, and melon (C. melo L., 2n=2x=24). Whole-genome comparisons revealed that C. hystrix is phylogenetically closer to cucumber than to melon, providing a molecular basis for the success of its hybridization with cucumber. Moreover, expanded gene families of C. hystrix were significantly enriched in "defense response," and C. hystrix harbored 104 nucleotide-binding site-encoding disease resistance gene analogs. Furthermore, 121 genes were positively selected, and 12 (9.9%) of these were involved in responses to biotic stimuli, which might explain the high disease resistance of C. hystrix. The alignment of whole C. hystrix genome with cucumber genome and self-alignment revealed 45,417 chromosome-specific sequences evenly distributed on C. hystrix chromosomes. Finally, we developed four cucumber-C. hystrix alien addition lines and identified the exact introgressed chromosome using molecular and cytological methods. The assembled C. hystrix genome can serve as a valuable resource for studies on Cucumis evolution and interspecific introgression breeding of cucumber.

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