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

Abstract

Transposable elements (TEs) are mobile genetic elements found in the majority of eukaryotic genomes. Because of their mobility in the host genome, TEs can deeply impact the structure and evolution of chromosomes and can induce mutations affecting coding genes. In response to these potential threats, host genomes use various processes to repress the TE expression, leading to an arm-race between TEs for their persistence and host genomes for their protection. In plants, the major group of TEs is the Long Terminal Repeats retrotransposons (LTR-RT). They are classified into superfamilies (Gypsy, Copia) and sub-classified into lineages according to similarities, structures and presence of coding domains. Among the different ways LTR-RTs can proliferate, horizontal transfer (HT), defined as the nonsexual transmission of nuclear and plastid genetic material between species, is a process allowing LTR-RTs to invade a new genome. Although this phenomenon was considered rare in eukaryotic organisms, recent studies demonstrate numerous potential transfers of LTR-RTs, suggesting that HT may be more frequent than initially estimated. This study aims to determine which LTR-RT lineages are shared with high similarity among 69 reference genomes that represent the major groups of green plants. We first 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) and very few of them included the Gypsy superfamily. Interestingly, a detailed analysis of three high similarities involving the Tork/Tar/Ikeros group of lineages indicates a patchy distribution of the elements and phylogenetic incongruities, indicating they originated from potential HTs. Overall, our results demonstrate that three specific lineages of Copia share outstanding similarity between very distant species and may probably be involved in horizontal transfer mechanisms.