Prunus zhengheensis Whole v1.0 Genome Assembly & Annotation

Publication

Haplotype-resolved genome of Prunus zhengheensis provides insight into its evolution and low temperature adaptation in apricot 
Wei Tan, Pengyu Zhou, Xiao Huang, Ruyu Liao, Xiaoan Wang, Yaoyao Wu, Zhaojun Ni, Ting Shi, Xiaqing Yu, Huiqin Zhang, Chengdong Ma, Feng Gao, Yufan Ma, Yang Bai, Faisal Hayat, Ouma Kenneth Omondi, Daouda Coulibaly, Zhihong Gao
Horticulture Research, Volume 11, Issue 4, April 2024, uhae103, https://doi.org/10.1093/hr/uhae103

Abstract

Prunus zhengheensis, an extremely rare population of apricots, originated in warm South-East China and is an excellent material for genetic breeding. However, most apricots and two related species (P. sibirica, P. mandshurica) are found in the cold northern regions in China and the mechanism of their distribution is still unclear. In addition, the classification status of P. zhengheensis is controversial. Thus, we generated a high-quality haplotype-resolved genome for P. zhengheensis, exploring key genetic variations in its adaptation and the causes of phylogenetic incongruence. We found extensive phylogenetic discordances between the nuclear and organelle phylogenies of P. zhengheensis, which could be explained by incomplete lineage sorting. A 242.22-Mb pan-genome of the Armeniaca section was developed with 13 chromosomal genomes. Importantly, we identified a 566-bp insertion in the promoter of the HSFA1d gene in apricot and showed that the activity of the HSFA1d promoter increased under low temperatures. In addition, HSFA1d overexpression in Arabidopsis thaliana indicated that HSFA1d positively regulated plant growth under chilling. Therefore, we hypothesized that the insertion in the promoter of HSFA1d in apricot improved its low-temperature adaptation, allowing it to thrive in relatively cold locations. 
The findings help explain the weather adaptability of Armeniaca plants.