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Dupeyron, M.

Publications and source records attributed to Dupeyron, M..

2 recordsLinked to original sources
bioRxiv2022

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

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.

genomics↗
bioRxiv2021

Broadscale evolutionary analysis of eukaryotic DDE transposons

DDE transposons are widespread selfish genetic elements, often comprising a large proportion of eukaryotic genomic content. DDE transposons have also made important contributions to varied host functions during eukaryotic evolution, and their transposases may be the most abundant and ubiquitous genes in nature. Yet much remains unknown about their basic biology. We employ a broadscale screen of DDE transposase diversity to characterise major evolutionary patterns for all 19 DDE transposon superfamilies. We identify considerable variation in DDE transposon superfamily size, and find a dominant association with animal hosts. While few DDE transposon superfamilies specialise in plants or fungi, the four largest superfamilies contain major plant-associated clades, at least partially underlying their relative success. We recover a pattern of host conservation among DDE transposon lineages, punctuated by occasional horizontal transfer to distantly related hosts. Host range and horizontal transfer are strongly positively correlated with DDE transposon superfamily size, arguing against variation in the capacity for generalism. We find that rates of horizontal transfer decrease sharply with increasing levels of host taxonomy, supporting the existence of host-associated barriers to DDE transposon spread. Overall, despite their relatively simple genetic structure, our results imply that trade-offs in host adaptation are important in defining DDE transposon-host relationships and evolution. In addition, our study provides a phylogenetic framework to facilitate the identification and further analysis of DDE transposons.

genomics↗