Haplotype-resolved genome assembly for tetraploid Chinese cherry (Prunus pseudocerasus) offers insights into fruit firmness

文献类型： 外文期刊

第一作者： Jiu, Songtao

作者： Jiu, Songtao;Lv, Zhengxin;Liu, Moyang;Xu, Yan;Zhang, Xinyu;Cao, Jun;Manzoor, Muhammad Aamir;Li, Fangdong;Li, Hongwen;Chen, Lijuan;Zhang, Xu;Wang, Shiping;Zhang, Caixi;Chen, Baozheng;Dong, Xiao;Xia, Mingxu;Dong, Yang;Xia, Mingxu;Li, Fangdong;Zhang, Xu;Li, Hongwen;Chen, Lijuan

作者机构：

期刊名称：HORTICULTURE RESEARCH （ 影响因子：7.6； 五年影响因子：8.2 ）

ISSN： 2662-6810

年卷期： 2024 年 11 卷 7 期

页码：

收录情况： SCI

摘要： Chinese cherry (Prunus pseudocerasus) holds considerable importance as one of the primary stone fruit crops in China. However, artificially improving its traits and genetic analysis are challenging due to lack of high-quality genomic resources, which mainly result from difficulties associated with resolving its tetraploid and highly heterozygous genome. Herein, we assembled a chromosome-level, haplotype-resolved genome of the cultivar 'Zhuji Duanbing', comprising 993.69 Mb assembled into 32 pseudochromosomes using PacBio HiFi, Oxford Nanopore, and Hi-C. Intra-haplotype comparative analyses revealed extensive intra-genomic sequence and expression consistency. Phylogenetic and comparative genomic analyses demonstrated that P. pseudocerasus was a stable autotetraploid species, closely related to wild P. pusilliflora, with the two diverging similar to 18.34 million years ago. Similar to other Prunus species, P. pseudocerasus underwent a common whole-genome duplication event that occurred similar to 139.96 million years ago. Because of its low fruit firmness, P. pseudocerasus is unsuitable for long-distance transportation, thereby restricting its rapid development throughout China. At the ripe fruit stage, P. pseudocerasus cv. 'Zhuji Duanbing' was significantly less firm than P. avium cv. 'Heizhenzhu'. The difference in firmness is attributed to the degree of alteration in pectin, cellulose, and hemicellulose contents. In addition, comparative transcriptomic analyses identified GalAK-like and Stv1, two genes involved in pectin biosynthesis, which potentially caused the difference in firmness between 'Zhuji Duanbing' and 'Heizhenzhu'. Transient transformations of PpsGalAK-like and PpsStv1 increase protopectin content and thereby enhance fruit firmness. Our study lays a solid foundation for functional genomic studies and the enhancement of important horticultural traits in Chinese cherries.

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