Horizontal Transfer of LTR Retrotransposons Contributes to the Genome Diversity of Vitis

Abstract

While horizontally transferred transposable elements (TEs) have been reported in several groups of plants, their importance for genome evolution remains poorly understood. To understand how horizontally transferred TEs contribute to plant genome evolution, we investigated the composition and activity of horizontally transferred TEs in the genomes of four Vitis species. A total of 35 horizontal transfer (HT) events were identified between the four Vitis species and 21 other plant species belonging to 14 different families. We determined the donor and recipient species for 28 of these HTs, with the Vitis species being recipients of 15 of them. As a result of HTs, 8–10 LTR retrotransposon clusters were newly formed in the genomes of the four Vitis species. The activities of the horizontally acquired LTR retrotransposons differed among Vitis species, showing that the consequences of HTs vary during the diversification of the recipient lineage. Our study provides the first evidence that the HT of TEs contributes to the diversification of plant genomes by generating additional TE subfamilies and causing their differential proliferation in host genomes.

Transposable elements: multifunctional players in the plant genome

“…LTR-RTs have low DNA copy numbers in the genome, and many are associated with DNA methylation, especially in heterochromatin regions, as seen in Beta vulgaris . In addition, LTR-RTs contribute to plant genome diversification, as reported in a study by Park et al. (2021) on genomes of Vitis species ( Cresse et al., 1995 ; Bennetzen, 2000 ; Zakrzewski et al., 2017 ; Park et al., 2021 ; Ramakrishnan et al., 2023 ).…”

“…In addition, LTR-RTs contribute to plant genome diversification, as reported in a study by Park et al. (2021) on genomes of Vitis species ( Cresse et al., 1995 ; Bennetzen, 2000 ; Zakrzewski et al., 2017 ; Park et al., 2021 ; Ramakrishnan et al., 2023 ).…”

The Madagascar palm genome provides new insights on the evolution of Apocynaceae specialized metabolism

“…The notable presence of TEs, especially LTR elements, in the P. lamerei (72.48%) and V. thouarsii (75.16% [ 62 ]) genomes raises questions about their role in shaping genomic architecture. It is likely that the common ancestor of these two species may have undergone horizontal transfer of TE, known to contribute to genome diversification [ 77 ]. This phenomenon could then have led to a sharp increase in genome size, which over time contracted through the removal of DNA in other Apocynaceae species such as C. roseus .…”

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

“…This observation is supported by the reclassification of the 32 LTR-RT horizontally transferred in plants (El Baidouri et al 2014) for which most of them (27) are Copia from Ivana/Oryco, Ale/Retrofit and Tork/Tar/Ikeros. Moreover, a re-analysis of the recent bibliography on plant HTs, indicates that Copia elements are clearly more frequently transferred than Gypsy (Dias et al 2015; Roulin et al 2007; 2009; Cheng et al 2009; Huang et al 2017; Hou et al 2018; Park et al 2021; Park, Christin, et Bennetzen 2021). Although classification data are not homogeneous, among the 175 cases of HT found in the literature, 65% of the LTR-RTs involved in HT are classified as Copia .…”