Data from: MITE annotation and landscape in 207 plant genomes reveal their evolutionary dynamics and functional roles

Miniature inverted-repeat transposable elements (MITEs) are short,
non-autonomous class II transposable elements prevalent in eukaryotic
genomes, contributing to various genomic and genic functions in plants.
However, research on MITEs mainly targets a few species, limiting a
comprehensive understanding and systematic comparison of MITEs in plants.
Here, we developed a highly sensitive MITE annotation pipeline with a low
false positive rate and applied it to 207 high-quality plant genomes. We
found over a 20,000-fold variation in MITE copy numbers among species,
with Gnetum montanum harboring the most. The Mutator superfamily is
widespread, comprising about 41.5%, whereas Tc1/Mariner and PIF/Harbinger
superfamilies expanded rapidly in monocots, particularly in Poaceae. The
analysis of MITE insertion times revealed an expansion around 30 million
years ago (Mya), peaking at 9−10 Mya, with some species showing another
ancient, slower expansion. In three representative families, we identified
much more species-specific MITE insertion sites than shared orthologous
ones, underscoring MITEs' significant role in genome diversity.
Phylogenomic analyses indicate that MITEs accumulated gradually and
specifically during speciation, primarily through new insertions, with
duplication as a secondary mechanism. MITEs tend to insert near genes,
particularly within 500−1000 bp of their flanking regions, and often
enhance gene expression. These insertions are associated with diverse gene
functions, mainly in transport, synthesis, and metabolism. Furthermore, we
identified 985 MITE-derived miRNAs from 392 families across 56 species,
mainly from Mutator, Tc1/Mariner, and PIF/Harbinger, targeting a variety
of gene functions. This study enhances our understanding of the evolution
and functional roles of MITEs in plants and provides a basis for exploring
their function in further research.