De novo gene integration into regulatory networks via interaction with conserved genes in peach

文献类型： 外文期刊

第一作者： Cao, Yunpeng

作者： Cao, Yunpeng;Zhao, Yun;Han, Yuepeng;Hong, Jiayi;Cai, Yongping;Li, Xiaoxu;Wang, Han;Zhang, Lin;Lin, Mengfei

作者机构：

期刊名称：HORTICULTURE RESEARCH （ 影响因子：8.5； 五年影响因子：9.1 ）

ISSN： 2662-6810

年卷期： 2024 年 11 卷 12 期

页码：

收录情况： SCI

摘要： De novo 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 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 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.

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