Horizontal transfers of LTR retrotransposons in seven species of Rosales

Abstract

Horizontal transposable element transfer (HTT) events have occurred among a large number of species and play important roles in the composition and evolution of eukaryotic genomes. HTTs are also regarded as effective forces in promoting genomic variation and biological innovation. In the present study, HTT events were identified and analyzed in seven sequenced species of Rosales using bioinformatics methods by comparing sequence conservation and K/K value of reverse transcriptase (RT) with 20 conserved genes, estimating the dating of HTTs, and analyzing the phylogenetic relationships. Seven HTT events involving long terminal repeat (LTR) retrotransposons, two HTTs between Morus notabilis and Ziziphus jujuba, and five between Malus domestica and Pyrus bretschneideri were identified. Further analysis revealed that these LTR retrotransposons had functional structures, and the copy insertion times were lower than the dating of HTTs, particularly in Mn.Zj.1 and Md.Pb.3. Altogether, the results demonstrate that LTR retrotransposons still have potential transposition activity in host genomes. These results indicate that HTT events are another strategy for exchanging genetic material among species and are important for the evolution of genomes.

Characterization of genome‐wide long terminal repeat retrotransposons provide insights into trait evolution of four grapevine species

“…. However, the number of intergenomic syntenic LTR retrotransposons can also be affected by environment, genetic background, and horizontal transfer (El Baidouri et al, 2014; Hou et al, 2018). In conclusion, combining the results of πN / πS value, phylogenetic tree, and syntenic analyses, many LTR retrotransposons among grapevine relatives were formed after species divergence through the duplication of limited common ancestral LTR retrotransposons (Figs. )…”

Molecular fossils illuminate the evolution of retroviruses following a macroevolutionary transition from land to water

“…Therefore, the timing of a single ERV integration event can be estimated by measuring the genetic distance between LTR sequences. The genetic distance between 5'-and 3'-LTRs of an ERV increases with its integration time [37,38]. To explore the temporal dynamics of the LTW ERV lineages, we retrieved all the complete LTW ERVs and calculated the genetic distance between their 5'-and 3'-LTRs (Fig 5A).…”

Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning

“…El Baidouri et al [119] demonstrated HTTs between at least 26 plant species. Hou et al [120] found HTT events among seven Rosales species. Dias et al [116] hypothesized the HTT of an LTR retrotransposon called “Copia25” between the ancestors of the genera Ixora and Musa .…”

“…Dias et al [116] hypothesized the HTT of an LTR retrotransposon called “Copia25” between the ancestors of the genera Ixora and Musa . Although the mechanisms of HTT remain unclear in plants, HTT represents an important way for host genomes to innovate and evolve [120].…”