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Genome
Article . 2023 . Peer-reviewed
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https://doi.org/10.1101/2022.0...
Article . 2022 . Peer-reviewed
Data sources: Crossref
Genome
Article . 2023
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High nucleotide similarity of three Copia lineage LTR retrotransposons among plant genomes

Authors: Simon Orozco-Arias; Mathilde Dupeyron; David Gutiérrez-Duque; Reinel Tabares-Soto; Romain Guyot;

High nucleotide similarity of three Copia lineage LTR retrotransposons among plant genomes

Abstract

Transposable elements (TEs) are mobile elements found in the majority of eukaryotic genomes. TEs deeply impact the structure and evolution of chromosomes and can induce mutations affecting coding genes. In plants, the major group of TEs is long terminal repeat retrotransposons (LTR-RTs). They are classified into superfamilies ( Gypsy, Copia) and subclassified into lineages. Horizontal transfer (HT), defined as the nonsexual transmission of genetic material between species, is a process allowing LTR-RTs to invade a new genome. Although this phenomenon was considered rare, recent studies demonstrate numerous transfers of LTR-RTs. This study aims to determine which LTR-RT lineages are shared with high similarity among 69 plant genomes. We identified and classified 88 450 LTR-RTs and determined 143 cases of high similarities between pairs of genomes. Most of them involved three Copia lineages ( Oryco/ Ivana, Retrofit/ Ale, and Tork/ Tar/ Ikeros). A detailed analysis of three cases of high similarities involving Tork/ Tar/ Ikeros group shows an uneven distribution in the phylogeny of the elements and incongruence with between phylogenetic trees topologies, indicating they could be originated from HTs. Overall, our results suggest that LTR-RT Copia lineages share outstanding similarity between distant species and may likely be involved in HT mechanisms more frequent than initially estimated.

Country
France
Keywords

plant genomes, 580, 570, Retroelements, Nucleotides, LTR retrotransposons, Terminal Repeat Sequences, bioinformatics, Evolution, Molecular, genomics, horizontal transfers, Phylogeny, Genome, Plant

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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
4
Average
Average
Average