title: Virus-like attachment sites as structural landmarks of plants retrotransposons.
abstract: BACKGROUND
  The 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.
  
  
  RESULTS
  Here 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.
  
  
  CONCLUSIONS
  The 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.
authors.affiliation: Departamento de Botânica, Instituto de Biociências (IB), Universidade de São Paulo (USP), 05508-090 São Paulo, SP Brasil.
authors.forename: Edgar Andres
authors.initials: EA
authors.lastname: Ochoa Cruz
authors.affiliation: Departamento de Botânica, Instituto de Biociências (IB), Universidade de São Paulo (USP), 05508-090 São Paulo, SP Brasil.
authors.forename: Guilherme Marcello Queiroga
authors.initials: GM
authors.lastname: Cruz
authors.affiliation: Departamento de Botânica, Instituto de Biociências (IB), Universidade de São Paulo (USP), 05508-090 São Paulo, SP Brasil.
authors.forename: Andréia Prata
authors.initials: AP
authors.lastname: Vieira
authors.affiliation: Departamento de Botânica, Instituto de Biociências (IB), Universidade de São Paulo (USP), 05508-090 São Paulo, SP Brasil.
authors.forename: Marie-Anne
authors.identifier: 0000-0002-6506-2734
authors.initials: MA
authors.lastname: Van Sluys
keywords: Angiosperm genomes; LTR-RTs; Retrotransposons; vl-att site