LTR retrotransposons shape genome architecture, function, and evolution in diverse plant species

Area of Science:

• Plant genomics
• Molecular evolution
• Transposable elements

Background:

• Long terminal repeat retrotransposons (LTR-RTs) are abundant in plant genomes, influencing genome structure and evolution.
• Understanding their chromosomal distribution and dynamics is crucial but remains incomplete.

Purpose of the Study:

• To investigate the abundance, spatial organization, and evolutionary history of intact LTR-RTs in plants.
• To analyze LTR-RT distribution patterns across chromosome identity, superfamilies, and lineages.

Main Methods:

• Analysis of high-quality chromosome-level genomes from 208 plant species.
• Utilized the MegaLTR tool for LTR-RT identification and analysis.
• Examined insertion time across genic and intergenic regions.

Main Results:

• Extensive interspecific variability in LTR-RT composition and chromosomal organization was observed.
• LTR-RT distributions are non-random and influenced by chromosome identity, superfamily (Copia vs. Ty3), and lineage.
• Ty3-retrotransposons show preferential accumulation in heterochromatic regions, while Copia elements exhibit more inter-chromosomal heterogeneity.
• Younger LTR-RT insertions are prevalent within genes, suggesting purifying selection removes older deleterious insertions from functional sequences.

Conclusions:

• LTR-RT chromosomal landscapes are shaped by superfamily-specific behavior, lineage history, and selective constraints.
• Regulatory mechanisms of LTR-RTs are broadly conserved, but their genomic impact is highly variable.
• Transposable elements play a central role in plant genome evolution.