Virus-like attachment sites as structural landmarks of plants retrotransposons

Author(s)

Ochoa Cruz, Edgar Andres ; Queiroga Cruz, Guilherme Marcello ; Vieira, Andreia Prata ; Van Sluys, Marie-Anne

• Document type: Journal article
• Source: MOBILE DNA; v. 7, JUL 28 2016.
• Web of Science Citations: 0

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. (AU)

• FAPESP's process: 12/21064-4 - Building a Synthetic Biology Platform for Functional Screening of Promoter Sequences in Plants
• Grantee: Edgar Andrés Ochoa Cruz
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 12/02671-7 - At-thi1 homologs in sugarcane: a molecular and functional study
• Grantee: Andréia Prata Vieira
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• FAPESP's process: 08/52074-0 - Sugarcane genome sequence: plant transposable elements are active contributors to gene structure variation, regulation and function
• Grantee: Marie-Anne Van Sluys
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Thematic Grants