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

Abstract

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.

Acknowledgements

We sincerely thank Prof. Hui Song from Qingdao Agricultural University for his valuable suggestions on the identification of de novo genes. We also express our gratitude to the editors and reviewers for their insightful comments and thorough review of our manuscript. This research was funded by the National Natural Science Foundation of China (Grant No. U23A20206 and Grant No. 32201602), the Natural Science Fund of Hubei Province (Grant No. 2023AFB1036 and Grant No. 2022CFB932), the Beijing Life Science Academy Project (Grant No. 2023200CC0270), the Key Special Project of Intergovernmental International Cooperation of the National Key R&D Program of China (Grant No. 2023YFE0125100), the Knowledge Innovation Program of Wuhan Basic Research (Grant No. 2022020801010167), and the China Agriculture Research System (Grant No. CARS-30).

Author contributions

Y.P.C. and Y.P.H. spearheaded the conception and design of the study. Y.P.C. was responsible for data analysis, drafting the manuscript, and incorporating revisions. Collaborative data analyses were performed by Y.P.C., J.Y.H., L.Z., X.X.L., X.F.F., H.W., L.Z., M.F.L., and Y.P.C. Both Y.P.C. and Y.P.H. critically reviewed and assessed the final manuscript.

Data availability

The RNA-seq project of peach (P. persica) has been deposited at the BIG Data Center (https://bigd.big.ac.cn/gsa) under the accession: PRJCA011988.

Conflict of Interests Statement

The authors declare that they have no competing interests.

Supplementary Data

Supplementary data is available at Horticulture Research online.

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