Characterization and Evolutionary Analyses of Terminal-Repeat Retrotransposons in Miniature (TRIMs) in Plants

Terminal-repeat retrotransposons in miniature (TRIMs) represent a unique group of LTR retrotransposons that are extremely small and difficult to identify. Thus far, only a few TRIMs have been characterized, and their evolutionary impact on host genomes is poorly understood.

We combined de novo and homology-based methods to annotate TRIMs in sequenced plant genomes. We identified 145 previously undescribed TRIMs, including the first TRIMs in a lycophyte and in non-vascular plants. The majority of the TRIM families were highly conserved and shared within and between plant families. Unlike most LTR retrotransposons, TRIMs are enriched in or near genes. TRIMs were targeted by both 21 and 24 nt small RNAs and frequently found in CG body methylated genes. Importantly, we identified putative autonomous retrotransposons and very recent transpositions of a TRIM element in O. sativa. Our data suggested that TRIMs are widely present in plant genomes and may have unique impacts on host genomes. The pipeline was also used to annotate animal genomes and we found TRIMs in the human, mouse and nematode.