New high-quality peach (Prunus persica L. Batsch) genome assembly to analyze the molecular evolutionary mechanism of volatile compounds in peach fruits.

Peach (Prunus persica L. Batsch) is an economically important fruit crop worldwide. Although a high-quality peach genome has previously been published, Sanger sequencing was used for its assembly, which generated short contigs. Here, we report a chromosome-level genome assembly and sequence analysis of Chinese Cling, an important founder cultivar for peach breeding programs worldwide. The assembled genome contained 247.33 Mb with a contig N50 of 4.13 Mb and a scaffold N50 of 29.68 Mb, representing 99.8% of the estimated genome. Comparisons between this genome and the recently published one (Lovell peach) uncovered 685 407 single nucleotide polymorphisms, 162 655 insertions and deletions, and 16 248 structural variants. Gene family analysis highlighted the contraction of the gene families involved in flavone, flavonol, flavonoid, and monoterpenoid biosynthesis. Subsequently, the volatile compounds of 256 peach varieties were quantitated in mature fruits in 2015 and 2016 to perform a genome-wide association analysis. A comparison with the identified domestication genomic regions allowed us to identify 25 quantitative trait loci, associated with seven volatile compounds, in the domestication region, which is consistent with the differences in volatile compounds between wild and cultivated peaches. Finally, a gene encoding terpene synthase, located within a previously reported quantitative trait loci region, was identified to be associated with linalool synthesis. Such findings highlight the importance of this new assembly for the analysis of evolutionary mechanisms and gene identification in peach species. Furthermore, this high-quality peach genome provides valuable information for future fruit improvement.