A miniature inverted-repeat transposable element, AddIn-MITE, located inside a WD40 gene is conserved in Andropogoneae grasses.

Clicia Grativol,Flavia Thiebaut,Sara Sangi,Walaci da Silva Santos,Patricia Montessoro,Adriana S. Hemerly,Paulo C.G. Ferreira

doi:10.7717/peerj.6080

Clicia Grativol, Flavia Thiebaut + Show 5 more

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https://doi.org/10.7717/peerj.6080

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Abstract

Miniature inverted-repeat transposable elements (MITEs) have been associated with genic regions in plant genomes and may play important roles in the regulation of nearby genes via recruitment of small RNAs (sRNA) to the MITEs loci. We identified eight families of MITEs in the sugarcane genome assembly with MITE-Hunter pipeline. These sequences were found to be upstream, downstream or inserted into 67 genic regions in the genome. The position of the most abundant MITE (Stowaway-like) in genic regions, which we call AddIn-MITE, was confirmed in a WD40 gene. The analysis of four monocot species showed conservation of the AddIn-MITE sequence, with a large number of copies in their genomes. We also investigated the conservation of the AddIn-MITE’ position in the WD40 genes from sorghum, maize and, in sugarcane cultivars and wild Saccharum species. In all analyzed plants, AddIn-MITE has located in WD40 intronic region. Furthermore, the role of AddIn-MITE-related sRNA in WD40 genic region was investigated. We found sRNAs preferentially mapped to the AddIn-MITE than to other regions in the WD40 gene in sugarcane. In addition, the analysis of the small RNA distribution patterns in the WD40 gene and the structure of AddIn-MITE, suggests that the MITE region is a proto-miRNA locus in sugarcane. Together, these data provide insights into the AddIn-MITE role in Andropogoneae grasses.

Highlights

Transposable elements (TEs) have important roles in plant genome evolution due to the high efficient copy number increase through a copy-and-paste and cut-and-paste mechanisms (Bennetzen, Ma & Devos, 2005; Bennetzen, 2007)
Once we found that the AddIn-Miniature inverted-repeat transposable elements (MITEs) was associated with sugarcane genic regions, we extended the analysis to other monocot genomes
We investigated the TE class II—MITEs—in sugarcane methyl-filtered genome assembly in sugarcane

Summary

Introduction

Transposable elements (TEs) have important roles in plant genome evolution due to the high efficient copy number increase through a copy-and-paste and cut-and-paste mechanisms (Bennetzen, Ma & Devos, 2005; Bennetzen, 2007). Since their first description as mobile elements by Barbara McClintock, TEs have been correlated with changes in chromosome structure and gene expression patterns (McClintock, 1950). Miniature inverted-repeat transposable elements (MITEs) are a special class of TEs with a structure similar to class II transposons, but without encoding transposase (Casacuberta & Santiago, 2003)

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