Newly Evolved Genes in Peach Offer Clues to Crop Adaptation

The emergence of new genes plays a critical role in driving species-specific traits and adaptive evolution. While gene duplication and fusion are well-known mechanisms, de novo gene birth-where functional genes evolve from noncoding sequences-is gaining recognition for its contribution to genetic novelty. These genes often have short lengths, low expression levels, and unique sequences, making them challenging to detect. Identifying them requires high-quality genome assemblies and comparative analysis with closely related species. Understanding their characteristics and integration into regulatory systems is essential for deciphering how new traits and functions evolve. Due to these challenges, deeper investigation into de novo genes is urgently needed.

Researchers from the Wuhan Botanical Garden of the Chinese Academy of Sciences and collaborating institutions published a new study (DOI: 10.1093/hr/uhae252) on September 5, 2024, in Horticulture Research. The study identified 178 de novo genes in Prunus persica 'baifeng' by comparing its genome to those of related Prunus species. Transcriptome analysis confirmed that 158 of these genes are actively expressed in various tissues. The findings shed light on how de novo genes integrate into plant regulatory networks and influence key processes such as growth, reproduction, and stress response.

The team used transcriptome sequencing and comparative genomics to identify de novo genes-those without orthologs in related species-that have emerged uniquely in peach. Out of 178 candidates, 158 genes were confirmed to be expressed in at least one tissue. These de novo genes showed distinct structural features compared to conserved genes: they were shorter, had fewer exons, and exhibited lower GC content and expression levels. Based on origin, they were divided into two types: Type I genes arose entirely from noncoding sequences and are enriched in plastid-related functions; Type II genes incorporated fragments of existing genes and were associated with development.

Gene ontology enrichment, cis-regulatory binding site analysis, and co-expression network mapping revealed that many de novo genes functionally integrate into the peach regulatory framework. Notably, some were co-expressed with conserved genes involved in stress response and development, and 25 were located within QTLs or MTLs associated with agronomic traits. This suggests that de novo genes are not only expressed but also biologically relevant, contributing to phenotypic variation and adaptive evolution in peach.

Our study demonstrates that de novo genes, once considered genetic noise, are in fact critical players in plant biology," said Dr. Yuepeng Han, senior author of the study. "By mapping their origin and function in peach, we show that these genes can quickly integrate into existing networks and potentially regulate key developmental traits. This research provides a template for exploring de novo gene evolution in other crops and highlights the dynamic nature of plant genomes."

Dr. Yuepeng Han, senior author of the study

This research marks the first comprehensive identification of de novo genes in peach and opens new avenues for crop improvement and evolutionary biology. By linking novel genes to regulatory pathways and agronomic traits such as fruit quality and stress tolerance, breeders may one day harness de novo genes for targeted breeding. Moreover, the findings contribute to our understanding of how plant genomes evolve new functions, offering valuable insights into the molecular basis of phenotypic diversity and adaptation across fruit species. Continued exploration could also reveal how these genes influence unique peach traits not seen in other Prunus relatives.