Recent amplification of microsatellite-associated miniature inverted-repeat transposable elements in the pineapple...

Area of Science:

• Genomics
• Molecular Evolution
• Bioinformatics

Background:

• Miniature inverted-repeat transposable elements (MITEs) are crucial for genome organization and evolution.
• Understanding MITEs in plant genomes, like pineapple, is essential for insights into genome structure and dynamics.

Purpose of the Study:

• To identify and characterize MITEs across the pineapple genome.
• To investigate the insertion preferences, origins, and evolutionary history of pineapple MITEs.
• To explore the impact of MITEs on gene expression and genome evolution.

Main Methods:

• Genome-wide identification and characterization of MITE families in the pineapple genome.
• Sequence similarity analysis of MITE families and their potential autonomous elements.
• Comparative analysis of microsatellite-targeting MITEs (mt-MITEs) and mutator-like MITEs (ml-MITEs).
• Epigenetic analysis and RNA-seq to assess MITE abundance and gene expression regulation.

Main Results:

• Identified abundant Ac-mMITEs (A. comosus microsatellite-associated MITEs) with a preference for (TA)n microsatellite regions.
• Ac-mMITEs likely originated from Mutator-like DNA transposons and exhibit polymorphic insertion sites.
• mt-MITEs showed lower host-induced silencing and higher abundance compared to ml-MITEs.
• Differential insertion preferences and impacts on nearby gene expression were observed between mt-MITEs and ml-MITEs.

Conclusions:

• Ac-mMITEs are the most abundant MITEs in the pineapple genome, derived from Mutator-like elements.
• Recent preferential insertion into microsatellites may be a host-coevolution strategy, promoting mt-MITE amplification.
• Minimal impact of mt-MITEs on gene expression may facilitate their amplification by evading genome control mechanisms.