Genomic evidence for evolutionary history and local adaptation of two endemic apricots: Prunus hongpingensis and P. zhengheensis

Abstract

Apricot, belonging to the Armeniaca section of Rosaceae, is one of the economically important crop fruits that has been extensively cultivated. The natural wild apricots offer valuable genetic resources for crop improvement. However, some of them are endemic, with small populations, and are even at risk of extinction. In this study we unveil chromosome-level genome assemblies for two southern China endemic apricots, Prunus hongpingensis (PHP) and P. zhengheensis (PZH). We also characterize their evolutionary history and the genomic basis of their local adaptation using whole-genome resequencing data. Our findings reveal that PHP and PZH are closely related to Prunus armeniaca and form a distinct lineage. Both species experienced a decline in effective population size following the Last Glacial Maximum (LGM), which likely contributed to their current small population sizes. Despite the observed decrease in genetic diversity and heterozygosity, we do not observe an increased accumulation of deleterious mutations in these two endemic apricots. This is likely due to the combined effects of a low inbreeding coefficient and strong purifying selection. Furthermore, we identify a set of genes that have undergone positive selection and are associated with local environmental adaptation in PHP and PZH, respectively. These candidate genes can serve as valuable genetic resources for targeted breeding and improvement of cultivated apricots. Overall, our study not only enriches our comprehension of the evolutionary history of apricot species but also offers crucial insights for the conservation and future breeding of other endemic species amidst rapid climate changes.

Acknowledgements

This work was supported by Science and Technology Projects of Shennongjia Academy of Forestry (SAF202104), the National Natural Science Foundation of China (32271824 and 31971676), and the Fundamental Research Funds for the Central Universities (2662019PY007). We would like to thank Dr Xiang Li (Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst) for his kind suggestions in bioinformatic analysis. The computations in this paper were run on the bioinformatics computing platform of the National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University.

Author contributions

J.D. and J.W. conceived and designed the research. S.X., S.Y., Z.W., Q.H., X.T., J.X., G.C., and X.D. performed the sampling and collected the materials. Y.Z. performed the genome assembly and annotation. T.Z. prepared DNA for sequencing. X.D. and S.X. conducted all bioinformatic analyses. X.D. wrote the manuscript, with input from J.D. and J.W. All authors read and edited the manuscript prior to publication.

Data availability statement

All Illumina sequence data of DNA raw data used in this study have been submitted to NCBI SRA, with accession number PRJNA957263. The whole-genome sequence and RNA data reported in this paper have been deposited in the Genome Warehouse at the National Genomics Data Center, Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, under accession number PRJCA019885.

Conflict of interests

The authors declare no competing interests.

Supplementary information

Supplementary data is available at Horticulture Research online.

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