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

作者：Songtao Jiu, Zhengxin Lv, Moyang Liu, Yan Xu, Baozheng Chen, Xiao Dong, Xinyu Zhang, Jun Cao, Muhammad Aamir Manzoor, Mingxu Xia, Fangdong Li, Hongwen Li, Lijuan Chen, Xu Zhang, Shiping Wang, Yang Dong, Caixi Zhang · 发表于：Horticulture Research · 年份：2024 · DOI：10.1093/hr/uhae142 · 被引用次数：19 · 研究领域：Plant Reproductive Biology、Plant Physiology and Cultivation Studies、Phytoplasmas and Hemiptera pathogens

Abstract 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 ~18.34 million years ago. Similar to other Prunus species, P. pseudocerasus underwent a common whole-genome duplication event that occurred ~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 an...