Chromosome-scale genome assembly of Prunus pusilliflora provides novel insights into genome evolution, disease resistance, and dormancy release in Cerasus L.

is a wild cherry germplasm resource distributed mainly in Southwest China. Despite its ornamental and economic value, a high-quality assembled genome is unavailable, hindering our understanding of its genetic background, population diversity, and evolutionary processes. Here, we assembled a chromosome-scale genome using Oxford Nanopore, Illumina, and chromosome conformation capture sequencing. The assembled genome size was 309.62 Mb, with 76 scaffolds anchored to eight pseudochromosomes. We predicted 33 035 protein-coding genes, functionally annotated 98.27% of them, and identified repetitive sequences covering 49.08% of the genome. We found that is closely related to and , having diverged from them ~41.8 million years ago. A comparative genomic analysis revealed that has 643 expanded and 1128 contracted gene families. Furthermore, we found that is more resistant to , , and pv. () DC3000 infections than cultivated . also has considerably more nucleotide-binding site-type resistance gene analogs than , which explains its stronger disease resistance. The cytochrome P450 and WRKY families of 263 and 61 proteins were divided into 42 and 8 subfamilies respectively in . Furthermore, 81 MADS-box genes were identified in , accompanying expansions of the SVP and AGL15 subfamilies and loss of the TM3 subfamily. Our assembly of a high-quality genome will be valuable for further research on cherries and molecular breeding.