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

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

doi:10.7717/peerj.6080

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

PeerJ. 2019 Jan 11:7:e6080. doi: 10.7717/peerj.6080. eCollection 2019.

Authors

Clicia Grativol¹, Flavia Thiebaut², Sara Sangi¹, Patricia Montessoro², Walaci da Silva Santos¹, Adriana S Hemerly², Paulo C G Ferreira²

Affiliations

¹ Laboratório de Química e Função de Proteínas e Peptídeos/Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil.
² Laboratório de Biologia Molecular de Plantas/Instituto de Bioquímica Médica Leopoldo De Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.

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.

Keywords: Andropogoneae; Genic region; MITEs; Maize; Small RNAs; Sorghum; Sugarcane; WD40 gene.

Grants and funding

This work was supported by the FAPERJ (Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro), CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico), CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior), INCT (Institutos Nacionais de Ciência e Tecnologia), FINEP (Financiadora de Estudos e Projetos) and the Newton Fund. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.