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

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.