Haplotype-resolved genome of Prunus zhengheensis provides insight into its evolution and low temperature adaptation in apricot

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.

Acknowledgements

We are grateful to Jiayan Zhang from the Fruit Science Institute of Liaoning Academy of Agricultural Sciences for manuscript review and the Bioinformatics Center of Nanjing Agricultural University for their technical support. This work was supported by the Jiangsu Seed Industry Key Research Program (JBGS [2021]019), the National Natural Science of China (32372670, 31971703), and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).

Author contributions

This study was designed by Z.G.Material was collected by X.H, P.Z., R.L., X.W., H.Z., Z.N., T.S., and W.T. Sample preparation and analysis were performed by C.M., F.G., Y.M., and Y.B. Data analysis was conducted by W.T. Author W.T. wrote the paper, and Y.W., X.Y., F.H., O.O., D.C., and Z.G.modified the language. All the authors read and approved the final manuscript.

Data availability

The assembled genome sequences of P. zhengheensis were deposited in the Genome Database for Rosaceae (https://www.rosaceae.org/).

Conflict of interest

The authors declare no conflict of interest.

Supplementary data

Supplementary data are available at Horticulture Research online.

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