Virus-like attachment sites as structural landmarks of plants retrotransposons

Abstract

BackgroundThe genomic data available nowadays has enabled the study of repetitive sequences and their relationship to viruses. Among them, long terminal repeat retrotransposons (LTR-RTs) are the largest component of most plant genomes, the Gypsy and Copia superfamilies being the most common. Recently it has been found that Del lineage, an LTR-RT of Gypsy superfamily, has putative virus-like attachment (vl-att) sites. This signature, originally described for retroviruses, is recognized by retroviral integrase conferring specificity to the integration process.ResultsHere we retrieved 26,092 putative complete LTR-RTs from 10 lineages found in 10 fully sequenced angiosperm genomes and found putative vl-att sites that are a conserved structural landmark across these genomes. Furthermore, we reveal that each plant genome has a distinguishable LTR-RT lineage amplification pattern that could be related to the vl-att sites diversity. We used these patterns to generate a specific quick-response (QR) code for each genome that could be used as a barcode of identification of plants in the future.ConclusionsThe universal distribution of vl-att sites represents a new structural feature common to plant LTR-RTs and retroviruses. This is an important finding that expands the information about the structural similarity between LTR-RT and retroviruses. We speculate that the sequence diversity of vl-att sites could be important for the life cycle of retrotransposons, as it was shown for retroviruses. All the structural vl-att site signatures are strong candidates for further functional studies. Moreover, this is the first identification of specific LTR-RT content and their amplification patterns in a large dataset of LTR-RT lineages and angiosperm genomes. These distribution patterns could be used in the future with biotechnological identification purposes.Electronic supplementary materialThe online version of this article (doi:10.1186/s13100-016-0069-5) contains supplementary material, which is available to authorized users.

Large-scale genome sequencing reveals the driving forces of viruses in microalgal evolution

“…in extant multicellular organisms, especially in plants, are thought to have viral origins (Galindo-Gonza ´lez et al, 2017;Gao et al, 2018;Krupovic and Koonin, 2015;Ochoa Cruz et al, 2016;Ustyantsev et al, 2017;Woodrow et al, 2012). Phylogenies created from these proteins and high-confidence homologs in NCBI (NR and Viral databases) revealed genetic exchange among species from unrelated clades.…”