Zhang Yangxin, Zhang Shuangyu, Guo Wenmeng, Zhang Yuxin, Chen Xiangxiang, Yu Qiaoming, Liu Yunxiao, Sun Yaqiang, Yu Ke, Li Houhua, Ma Fengwang, Zhao Tao
State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, People's Republic of China.
Research Institute for Landscape and Ornamental Plant, College of Landscape Architecture and Art, Northwest A&F University, Yangling, Shaanxi, People's Republic of China.
Plant Biotechnol J. 2025 Sep;23(9):3581-3596. doi: 10.1111/pbi.70167. Epub 2025 Jun 8.
Pseudocydonia sinensis, commonly known as Chinese quince, belongs to the Rosaceae family and is closely related to apple and pear. Despite its botanical significance, genomic resources for this species remain limited. We present a high-quality, chromosome-scale, and haplotype-resolved genome assembly of P. sinensis, characterized by high BUSCO completeness and QV scores. The genome sizes of Haplotypes A and B are 581.29 Mb and 561.80 Mb, respectively, each spanning 17 chromosomes with a contig N50 of 15.76 Mb. Comparative genomic analyses place P. sinensis within the Maleae tribe, closely related to Malus domestica and Pyrus communis, both of which have undergone an additional whole-genome duplication event. Gene family and metabolomic analyses show that the genome has an expansion of 1603 gene families, with an accumulation of secondary metabolites such as flavonoids and phenolic acids (e.g. rutin and caffeoylquinic acid). This duplication has contributed to the expansion of gene families involved in secondary metabolite biosynthesis, particularly in the phenylpropanoid and flavonoid pathways. Integrative transcriptomic and metabolomic analyses further revealed the MYB transcription factor ODORANT1 (ODO1) is a key regulator of phenylpropanoid metabolism. Functional assays show that PsMYBODO1 directly binds to and activates the promoters of key genes in this pathway, including PsRT3, PsPAL, PsCAD and PsCOMT. This high-quality reference genome provides a valuable resource for functional genomic studies and breeding programmes aimed at enhancing the medicinal properties of P. sinensis.
榅桲，俗称中国木瓜，属于蔷薇科，与苹果和梨亲缘关系密切。尽管其具有植物学意义，但其基因组资源仍然有限。我们展示了一个高质量、染色体水平且单倍型解析的榅桲基因组组装，其特征在于具有高BUSCO完整性和QV分数。单倍型A和B的基因组大小分别为581.29 Mb和561.80 Mb，均跨越17条染色体，重叠群N50为15.76 Mb。比较基因组分析表明，榅桲属于梨族，与苹果和西洋梨亲缘关系密切，后两者都经历了一次额外的全基因组复制事件。基因家族和代谢组学分析表明，该基因组有1603个基因家族发生了扩张，积累了黄酮类和酚酸类（如芦丁和咖啡酰奎尼酸）等次生代谢物。这种复制促进了参与次生代谢物生物合成的基因家族的扩张，特别是在苯丙烷类和黄酮类途径中。整合转录组学和代谢组学分析进一步揭示，MYB转录因子ODORANT1（ODO1）是苯丙烷类代谢的关键调节因子。功能分析表明，PsMYBODO1直接结合并激活该途径中关键基因的启动子，包括PsRT3、PsPAL、PsCAD和PsCOMT。这个高质量的参考基因组为旨在增强榅桲药用特性的功能基因组学研究和育种计划提供了宝贵资源。
