Miniature inverted repeat transposable elements in the genome of sugar beet and their impact on gene expression

TL;DR

This study maps MITEs in the sugar beet genome and shows how they influence gene expression, especially in regulatory regions.

Contribution

The first comprehensive annotation of MITEs in the sugar beet genome and their link to gene expression regulation.

Findings

MITEs cover 3% of the sugar beet genome, with Stowaway-like elements being the most common.

Over 60% of MITEs are located in genic regions, suggesting a role in gene regulation.

MITE insertions are associated with differentially expressed genes in sugar beet families.

Abstract

Miniature inverted-repeat transposable elements (MITEs) are the most abundant group among class II mobile elements in plant genomes. They are frequently located in gene-rich regions, which may affect gene structure and expression, leading to functional diversity. Our research aimed to perform a comprehensive global annotation of MITEs in the sugar beet genome, which has been lacking to date. We also attempted to elucidate the association between the presence of MITE insertions and the regulation of gene expression. Analysis of the MITEs distribution in sugar beet revealed that MITEs cover about 3% of the genome, with the largest group comprising Stowaway-like elements. Approximately 60% of all identified MITEs were located within genic regions, indicating their potential impact on gene expression regulation. Stowaway and Tourist-like elements were frequently present in introns and downstream from genes. Tourists were also relatively more enriched in 3’UTRs than the other MITE groups. hAT-like MITEs were present mainly in introns and 5’UTRs, while Mutator-like elements were relatively more frequently located in 5’UTRs than in the other MITE groups. Our study also showed that a considerable portion of the differentially expressed genes in plants from two F2 sugar beet families was associated with MITEs, especially Stowaways and Tourists. We provided a comprehensive landscape of MITE distribution in the sugar beet genome and described examples of MITE insertions located in the regulatory regions of genes that show significant differential expression. These results will facilitate research into the role of MITEs in their potential impact on gene expression regulation.

The online version contains supplementary material available at 10.1038/s41598-025-32772-7.

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