Tandem LTR-retrotransposon structures are common and highly polymorphic in plant genomes

Area of Science:

• Genomics
• Molecular Evolution
• Bioinformatics

Background:

• Long terminal repeat retrotransposons (LTR-RTs) are major components of plant genomes, driving genome evolution.
• Most LTR-RTs exist as defective, truncated copies or complex structures.
• Advancements in long-read sequencing enable detailed characterization of these complex LTR-RT structures.

Purpose of the Study:

• To characterize complex LTR-RT structures in plant genomes.
• To investigate the formation and prevalence of tandem LTR-RT arrays.
• To develop computational tools for identifying these structures.

Main Methods:

• Detailed analysis of rice loci with complex LTR-RT structures.
• Development of the IDENTAM computational pipeline for identifying tandem LTR-RTs.
• Application of IDENTAM to rice, Arabidopsis, almond, and cotton genomes.
• Utilizing graph-based pangenomic methodologies for resolving complex variations.

Main Results:

• Identified tandem arrays of LTR copies sharing internal LTRs, likely arising from single insertions.
• Gypsy elements appear more prone to forming these tandem structures.
• These tandem LTR-RT structures are highly polymorphic in rice, contributing to genetic variability.
• Detected 266 tandem LTR-RTs in a rice pangenome, indicating their frequency and polymorphism.
• Confirmed the prevalence of LTR-RT tandems across diverse plant genomes (Arabidopsis, almond, cotton).

Conclusions:

• LTR-RT elements can form tandem arrays.
• These tandem LTR-RT structures are abundant and highly polymorphic in rice.
• Tandem LTR-RT structures are widespread in the plant kingdom.
• Further research is needed to understand their origin and functional impact on genetic variability.