<i>De novo</i> gene integration into regulatory networks via interaction with conserved genes in peach

<i>De novo</i> genes can evolve "from scratch" from noncoding sequences, acquiring novel functions in organisms and integrating into regulatory networks during evolution to drive innovations in important phenotypes and traits. However, identifying <i>de novo</i> genes is challenging, as it requires high-quality genomes from closely related species. According to the comparison with nine closely related <i>Prunus</i> genomes, we determined at least 178 <i>de novo</i> genes in <i>P. persica</i> "baifeng". The distinct differences were observed between <i>de novo</i> and conserved genes in gene characteristics and expression patterns. Gene ontology enrichment analysis suggested that Type I <i>de novo</i> genes originated from sequences related to plastid modification functions, while Type II genes were inferred to have derived from sequences related to reproductive functions. Finally, transcriptome sequencing across different tissues and developmental stages suggested that <i>de novo</i> genes have been evolutionarily recruited into existing regulatory networks, playing important roles in plant growth and development, which was also supported by WGCNA analysis and quantitative trait loci data. This study lays the groundwork for future research on the origins and functions of genes in <i>Prunus</i> and related taxa.