Virus-like Attachment Sites as Structural Landmarks of Plants Retrotransposons

The genomic data available nowadays has enabled the study of repetitive sequences and their relationship to viruses. Among the repetitive sequences, long terminal repeat retrotransposons (LTR-RTs) are the largest component of most plant genomes, the Gypsy and Copia superfamilies being the most prevalent. Our group has retrieved 26,092 putative complete LTR-RTs from 10 lineages in 10 fully sequenced angiosperm genomes (Arabidopsis thaliana, Brachypodium distachyon, Glycine max, Medicago truncatula, Populus trichocarpa, Oryza sativa, Setaria italica, Sorghum bicolor, Vitis vinifera and Zea mays). Based on HMM models, plotcon and phylogenetic signatures we identified putative lineage specific virus-like attachment (vl-att) sites and structural landmarks conserved across these genomes. This signature, originally described for retroviruses, is recognized by retroviral integrase, which confers specificity to the integration process. Remarkably, each plant genome has a distinct LTR-RT lineage amplification pattern that can be related to the vl-att sites diversity. These patterns produce a specific quick-response (QR) code for each genome. All the structural vl-att site signatures are strong candidates for functional studies. We focused on 2432 Del elements that are organized into three clusters in plants. Each cluster is composed of elements with distinct LTR features, including lineage specific CpG island patterns. Further, based on the universal distribution of LTR-RTs, we investigated the Anemopaegmaspecies complex LTR-RT genome component and reveal that each plant genome has a distinct LTR-RT lineage amplification pattern, supporting Barbara McClintock`s understanding that these elements may underlie some species formation.

Financial support: FAPESP and CNPq