Virus-like attachment sites and plastic CpG islands:landmarks of diversity in plant Del retrotransposons.
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.
Departamento de Botânica, Instituto de Biociências (IB), Universidade de São Paulo (USP), São Paulo, São Paulo, Brasil.
Guilherme M Q
GM
Cruz
Departamento de Botânica, Instituto de Biociências (IB), Universidade de São Paulo (USP), São Paulo, São Paulo, Brasil.
Cushla J
CJ
Metcalfe
Universidade Federal do ABC (UFABC), São André, São Paulo, Brasil.
Nathalia
N
de Setta
Departamento de Botânica, Instituto de Biociências (IB), Universidade de São Paulo (USP), São Paulo, São Paulo, Brasil.
Edgar A O
EA
Cruz
Departamento de Botânica, Instituto de Biociências (IB), Universidade de São Paulo (USP), São Paulo, São Paulo, Brasil.
Andréia Prata
AP
Vieira
Departamento de Botânica, Instituto de Biociências (IB), Universidade de São Paulo (USP), São Paulo, São Paulo, Brasil.
Rosario
R
Medina
Departamento de Botânica, Instituto de Biociências (IB), Universidade de São Paulo (USP), São Paulo, São Paulo, Brasil.
Marie-Anne
MA
Van Sluys
D001482:Base Composition; D001483:Base Sequence; D005075:Biological Evolution; D018899:CpG Islands; D018745:Genome, Plant; D019684:Magnoliopsida / Q000145:classification / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D018626:Retroelements; D012190:Retroviridae / Q000235:genetics; D020079:Terminal Repeat Sequences
D018626:Retroelements