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Stones in genomic storms: transposable element-driven variation in Prunus fruit trees.

Attila Hegedűs¹, Beti Ivanovska², Júlia Halász²

¹Institute of Genetics and Biotechnology, Department of Plant Biotechnology, Horticultural Plant Genetics Group, Hungarian University of Agriculture and Life Sciences, Ménesi út 44, Budapest, 1118, Hungary. genetics.prunus@gmail.com.

|May 13, 2026

Summary

Transposable elements (TEs) significantly shape Prunus genomes, influencing traits and evolution. Advances in sequencing reveal their roles in diversification and potential for crop improvement.

Keywords:

Prunus Genome evolution Molecular markers Mutations Phenotypic diversity Regulation Retrotransposons Self-incompatibility Transposable elements Transposons

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Area of Science:

Genomics
Evolutionary Biology
Plant Science

Background:

Transposable elements (TEs) are key components of plant genomes, driving structural and functional diversification.
In Prunus species (peach, almond, apricot, cherry, plum), TEs comprise over half the genome, influencing evolutionary paths and traits.

Purpose of the Study:

To synthesize current knowledge on TE composition, evolutionary dynamics, and functional impacts in Prunus.
To highlight how advanced sequencing and annotation methods have improved understanding of TEs in Prunus.

Main Methods:

Review of existing literature on Transposable Elements in Prunus species.
Analysis of data from long-read sequencing technologies.
Application of structure-aware annotation pipelines for TE identification.

Main Results:

Both Class I retrotransposons and Class II DNA transposons contribute to genome expansion, gene duplication, and regulatory innovation in Prunus.
TE insertions impact various traits, including flowering time, fruit characteristics, and self-incompatibility, via epigenetic mechanisms.
Recent TE bursts are linked to hybridization, polyploidization, and adaptation, driving Prunus genome diversification.

Conclusions:

TEs are crucial drivers of Prunus genome evolution and phenotypic diversity.
TE insertion polymorphisms offer valuable molecular markers for Prunus diversity assessment, phylogenetics, and breeding.
Further integration of TE mapping with functional and epigenetic studies will unlock their potential for crop improvement.