De novo genes can evolve 'from scratch' from non-coding sequences, acquiring novel functions in organisms and integrating into regulatory networks during evolution to drive innovations in important phenotypes and traits. However, identifying de novo genes is challenging, as it requires high-quality genomes from closely related species. According to the comparison with nine closely related Prunus genomes, we determined at least 178 de novo genes in P. persica ‘baifeng’. The distinct differences were observed between de novo and conserved genes in gene characteristics and expression patterns. Gene ontology (GO) enrichment analysis suggested that Type I de novo 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 de novo 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 Prunus and related taxa.

中文翻译：

---

通过与桃中保守基因的相互作用将基因从头整合到调控网络中


从头基因可以从非编码序列“从头开始”进化，在生物体中获得新的功能，并在进化过程中整合到调控网络中，以推动重要表型和性状的创新。然而，从头识别基因具有挑战性，因为它需要来自密切相关物种的高质量基因组。根据与9个密切相关的李属基因组的比较，我们在桃“白凤”中确定了至少178个从头基因。在基因特征和表达模式方面观察到新生基因和保守基因之间的明显差异。基因本体（GO）富集分析表明，I型从头基因源自与质体修饰功能相关的序列，而II型基因被推断源自与生殖功能相关的序列。最后，跨不同组织和发育阶段的转录组测序表明，从头基因已被进化招募到现有的调控网络中，在植物生长和发育中发挥重要作用，这也得到了 WGCNA 分析和数量性状基因座数据的支持。这项研究为未来研究李属及相关类群基因的起源和功能奠定了基础。