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

Abstract

<i>Prunus pusilliflora</i> is a wild cherry germplasm resource distributed mainly in Southwest China. Despite its ornamental and economic value, a high-quality assembled <i>P. pusilliflora</i> genome is unavailable, hindering our understanding of its genetic background, population diversity, and evolutionary processes. Here, we <i>de novo</i> assembled a chromosome-scale <i>P. pusilliflora</i> 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 <i>P. pusilliflora</i> is closely related to <i>Prunus serrulata</i> and <i>Prunus yedoensis</i>, having diverged from them ~41.8 million years ago. A comparative genomic analysis revealed that <i>P. pusilliflora</i> has 643 expanded and 1128 contracted gene families. Furthermore, we found that <i>P. pusilliflora</i> is more resistant to <i>Colletotrichum viniferum</i>, <i>Phytophthora capsici</i>, and <i>Pseudomonas syringae</i> pv. <i>tomato</i> (<i>Pst</i>) DC3000 infections than cultivated <i>Prunus avium</i>. <i>P. pusilliflora</i> also has considerably more nucleotide-binding site-type resistance gene analogs than <i>P. avium</i>, 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 <i>P. pusilliflora</i>. Furthermore, 81 MADS-box genes were identified in <i>P. pusilliflora</i>, accompanying expansions of the SVP and AGL15 subfamilies and loss of the TM3 subfamily. Our assembly of a high-quality <i>P. pusilliflora</i> genome will be valuable for further research on cherries and molecular breeding.