Distribution of Small RNAs Along Transposable Elements in Vitis vinifera During Somatic Embryogenesis

Silvia Rotunno; Paola Leonetti; György Szittya; Vitantonio Pantaleo

doi:10.1007/978-1-0716-3515-5_19

Distribution of Small RNAs Along Transposable Elements in Vitis vinifera During Somatic Embryogenesis

Methods Mol Biol. 2024:2732:279-286. doi: 10.1007/978-1-0716-3515-5_19.

Authors

Silvia Rotunno¹, Paola Leonetti², György Szittya³, Vitantonio Pantaleo⁴

Affiliations

¹ Institute for Sustainable Plant Protection, National Research Council, Torino, Italy.
² Institute for Sustainable Plant Protection, National Research Council, Bari, Italy.
³ Institute of Genetics and Biotechnology, Hungarian University of Agricultural and Life Sciences, Gödöllő, Hungary.
⁴ Institute for Sustainable Plant Protection, National Research Council, Bari, Italy. vitantonio.pantaleo@cnr.it.

PMID: 38060132
DOI: 10.1007/978-1-0716-3515-5_19

Abstract

Metaviridae is a family of reverse-transcribing viruses, closely related to retroviruses; they exist within their host's DNA as transposable elements. Transposable element study requires the use of specialized tools, in part because of their repetitive nature. By combining data from transcript RNA-Seq, small RNA-Seq, and parallel analysis of RNA ends-Seq from grapevine somatic embryos, we set up a bioinformatics flowchart that could be able to assemble and identify transposable elements.

Keywords: Degradome; Small RNAs; Somatic embryos; Transposable elements; Vitis vinifera.

MeSH terms

DNA Transposable Elements* / genetics
RNA
Vitis* / genetics

Substances

DNA Transposable Elements
RNA