Discovery of De Novo Genes Sheds Light on Peach Evolution and Traits

The emergence of new genes is a central driver of evolutionary innovation. While mechanisms such as duplication and horizontal gene transfer have been widely studied, de novo gene birth represents a unique pathway where functional genes arise from noncoding DNA. These genes often display shorter lengths, lower expression levels, and tissue-specific functions, making them difficult to detect. Advances in genome sequencing have enabled systematic discovery of de novo genes across organisms, revealing roles in growth, reproduction, and stress response. However, questions remain about how these genes integrate into existing gene networks and contribute to agronomic traits. Due to these challenges, in-depth research on peach de novo genes is needed.

Researchers from the Chinese Academy of Sciences and collaborating institutions published (DOI: 10.1093/hr/uhae252) their findings on September 5, 2024, in Horticulture Research. Using high-quality genomes of multiple Prunus species, the team identified and characterized de novo genes in peach cultivar "baifeng". Their analysis revealed how these genes, absent in closely related genomes, have become transcriptionally active and functionally integrated. The study provides the first systematic evidence of de novo genes in peach, offering fresh insight into how fruit crops evolve novel traits and adapt to changing environments.

The team conducted comparative genomic analyses across nine Prunus genomes to pinpoint DNA sequences unique to peach that lacked homologs in related species. This yielded 178 candidate de novo genes, 158 of which were confirmed to be transcriptionally active. These genes were unevenly distributed across the peach's eight chromosomes, with the highest density on Chr1. Structural comparisons revealed that de novo genes were shorter, had fewer exons, lower GC content, and narrower expression ranges than conserved genes. Based on sequence origins, two categories were identified: Type I genes from purely noncoding regions and Type II from chimeric sequences containing fragments of existing genes. Gene ontology analysis showed Type I genes linked to plastid modification, while Type II genes were associated with growth and reproduction. Transcriptomic data and weighted gene co-expression network analysis (WGCNA) confirmed that de novo genes cluster with conserved genes in regulatory modules tied to photosynthesis, seed germination, stress response, and fruit development. Moreover, 25 de novo genes were mapped to quantitative trait loci (QTLs) related to growth and fruit quality, suggesting functional roles in shaping agronomic traits.

De novo genes are often overlooked because they emerge from noncoding DNA and lack evolutionary history. Our study shows that these genes are not only real but also play crucial roles in peach development and reproduction. By integrating into existing gene networks, de novo genes can influence key agronomic traits, from plastid function to fruit quality. This discovery deepens our understanding of how new traits arise in perennial crops and opens opportunities to harness these genes for breeding and improvement."

Yuepeng Han, lead author

The identification of de novo genes in peach offers valuable insight into the genetic basis of crop innovation. These genes could serve as untapped resources for improving fruit quality, stress tolerance, and adaptability in breeding programs. Because some are located in QTLs linked to seed size, growth habit, and fruit characteristics, they may represent novel targets for molecular breeding. More broadly, this work underscores the evolutionary importance of de novo genes in generating diversity across plants. By decoding how such genes integrate into regulatory networks, researchers can better predict and manipulate traits critical for agriculture and food security.