Virus-Like Attachment Sites and Plastic CpG Islands: Landmarks of Diversity in Plant Del Retrotransposons

Abstract

Full-length Del elements from ten angiosperm genomes, 5 monocot and 5 dicot, were retrieved and putative attachment (att) sites were identified. In the 2432 Del elements, two types of U5 att sites and a single conserved type of U3 att site were identified. Retroviral att sites confer specificity to the integration process, different att sites types therefore implies lineage specificity. While some features are common to all Del elements, CpG island patterns within the LTRs were particular to lineage specific clusters. All eudicot copies grouped into one single clade while the monocots harbour a more diverse collection of elements. Furthermore, full-length Del elements and truncated copies were unevenly distributed amongst chromosomes. Elements of Del lineage are organized in plants into three clusters and each cluster is composed of elements with distinct LTR features. Our results suggest that the Del lineage efficiently amplified in the monocots and that one branch is probably a newly emerging sub-lineage. Finally, sequences in all groups are under purifying selection. These results show the LTR region is dynamic and important in the evolution of LTR-retrotransposons, we speculate that it is a trigger for retrotransposon diversification.

Virus-like attachment sites as structural landmarks of plants retrotransposons

“…The Tar and Athila lineages exhibited a conserved nucleotide stretch of five bases and an additional conserved nucleotide outside this region. Our results are compatible with the length reported for the structural vl-att sites from the Del lineage (10 bp-11 bp) [ 19 ]. Long segments presenting high similarity levels were detected in Angela (18 bp-10 bp), Maximus (16 bp-5 bp), and CRM (12 bp-10 bp), making it more difficult to establish the correct length of the structural vl-att sites of these lineages.…”

“…In order to have a representative sample of the angiosperm genomes, we used the five eudicot ( Arabidopsis thaliana, Medicago truncatula, Populus trichocarpa, Vitis vinifera and Glycine max ) and the five monocot species ( Brachypodium dystachyon, Oryza sativa , Setaria italica, Sorghum bicolor, and Zea mays ) examined previously by our group [ 19 ]. They were analyzed with the LTR_STRUC software [ 22 ], which finds full length LTR-RT elements based on structural and sequence criteria.…”

“…The promoter and other regulatory sequences are located within U3 [ 23 ]. The vl-att should be at the beginning of the 5′ U3 region and at the end of the 3′ U5 region [ 19 ]. Using WebLogo and PlotCon [ 24 , 25 ] to analyze the 40 initial and terminal bases from the LTRs we identified conserved regions for most of the lineages (Fig.…”

“…Our research on the relationship between retroviruses and LTR-RTs has recently revealed that Del has putative virus-like attachment ( vl-att ) sites in its LTRs [ 17 – 19 ]. The LTRs are direct repeat sequences located at the 5′ and 3′ ends of the LTR-RT elements containing the regulatory information of the LTR-RT such as promoters, enhancers and termination signals [ 20 ].…”

“…We questioned whether vl-att sites are specific to the Del lineage or are conserved structural landmarks across plant LTR-RTs and, therefore, a new structural feature common to plant LTR-RTs and retroviruses. To study this hypothesis, we retrieved all the putative complete elements, a total of 26,092 elements, from the other LTR-RTs lineages present in the 10 angiosperm genomes used previously to study the Del lineage [ 19 ].…”