Landscape and evolutionary dynamics of terminal-repeat retrotransposons in miniature (TRIMs) in 48 whole plant genomes

Abstract

Terminal-repeat retrotransposons in miniature (TRIMs) are structurally similar to long terminal repeat (LTR) retrotransposons except that they are extremely small and difficult to identify. Thus far, only a few TRIMs have been characterized in the euphyllophytes and the evolutionary and biological impacts and transposition mechanism of TRIMs are poorly understood. In this study, we combined de novo and homology-based methods to annotate TRIMs in 48 plant genome sequences, spanning land plants to algae. We found 156 TRIM families, 146 previously undescribed. Notably, we identified the first TRIMs in a lycophyte and non-vascular plants. The majority of the TRIM families were highly conserved and shared within and between plant families. Even though TRIMs contribute only a small fraction of any plant genome, they are enriched in or near genes and may play important roles in gene evolution. TRIMs were frequently organized into tandem arrays we called TA-TRIMs, another unique feature distinguishing them from LTR retrotransposons. Importantly, we identified putative autonomous retrotransposons that may mobilize specific TRIM elements and detected very recent transpositions of a TRIM in O. sativa. Overall, this comprehensive analysis of TRIMs across the entire plant kingdom provides insight into the evolution and conservation of TRIMs and the functional roles they may play in gene evolution.