MITE Annotation and Landscape in 207 Plant Genomes Reveal Their Evolutionary Dynamics and Functional Roles

Area of Science:

• Genomics
• Molecular Biology
• Plant Science

Background:

• Miniature inverted-repeat transposable elements (MITEs) are widespread in eukaryotic genomes and play roles in genomic and genic functions in plants.
• Current research on plant MITEs is limited to a few species, hindering comprehensive understanding and comparative analyses.

Purpose of the Study:

• To develop a sensitive MITE annotation pipeline for large-scale plant genome analysis.
• To systematically investigate the distribution, evolution, and functional impact of MITEs across diverse plant species.

Main Methods:

• Developed a high-sensitivity MITE annotation pipeline with a low false positive rate.
• Applied the pipeline to 207 high-quality plant genomes.
• Conducted insertion time analysis, phylogenomic analyses, and identified MITE-derived microRNAs.

Main Results:

• Discovered over a 20,000-fold variation in MITE copy numbers across plant species.
• Identified Mutator, Tc1/Mariner, and PIF/Harbinger as major MITE superfamilies, with rapid expansion in monocots.
• Showed MITEs preferentially insert near genes, potentially enhancing gene expression, and identified 985 MITE-derived miRNAs.
• Found MITEs accumulate during speciation, primarily through recent insertions, contributing significantly to genome diversity.

Conclusions:

• This study provides a comprehensive overview of MITE evolution and distribution in plants.
• MITEs are dynamic elements contributing to plant genome diversity, gene regulation, and novel miRNA formation.
• The findings establish a foundation for future research into the functional roles of MITEs in plants.