Characterization of the LTR retrotransposon repertoire of a plant clade of six diploid and one tetraploid species

Plant J. 2013 Aug;75(4):699-709. doi: 10.1111/tpj.12233. Epub 2013 Jun 3.

Abstract

Comparisons of closely related species are needed to understand the fine-scale dynamics of retrotransposon evolution in flowering plants. Towards this goal, we classified the long terminal repeat (LTR) retrotransposons from six diploid and one tetraploid species of Orobanchaceae. The study species are the autotrophic, non-parasitic Lindenbergia philippensis (as an out-group) and six closely related holoparasitic species of Orobanche [O. crenata, O. cumana, O. gracilis (tetraploid) and O. pancicii] and Phelipanche (P. lavandulacea and P. ramosa). All major plant LTR retrotransposon clades could be identified, and appear to be inherited from a common ancestor. Species of Orobanche, but not Phelipanche, are enriched in Ty3/Gypsy retrotransposons due to a diversification of elements, especially chromoviruses. This is particularly striking in O. gracilis, where tetraploidization seems to have contributed to the Ty3/Gypsy enrichment and led to the emergence of seven large species-specific families of chromoviruses. The preferential insertion of chromoviruses in heterochromatin via their chromodomains might have favored their diversification and enrichment. Our phylogenetic analyses of LTR retrotransposons from Orobanchaceae also revealed that the Bianca clade of Ty1/Copia and the SMART-related elements are much more widely distributed among angiosperms than previously known.

Keywords: LTR retrotransposons; Orobanchaceae; Orobanche; Phelipanche; Ty1/Copia; Ty3/Gypsy; genome downsizing; next-generation sequencing; polyploidy; transposable elements.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA, Plant / chemistry
  • DNA, Plant / genetics
  • Diploidy
  • Evolution, Molecular
  • Genome, Plant / genetics*
  • High-Throughput Nucleotide Sequencing
  • Molecular Sequence Data
  • Orobanchaceae / genetics*
  • Phylogeny
  • Retroelements / genetics*
  • Sequence Analysis, DNA
  • Species Specificity
  • Terminal Repeat Sequences / genetics*
  • Tetraploidy

Substances

  • DNA, Plant
  • Retroelements

Associated data

  • GENBANK/AC018929
  • GENBANK/AC161750
  • GENBANK/AC232487
  • GENBANK/AF275345
  • GENBANK/AH013750
  • GENBANK/AM477556
  • GENBANK/AP009656
  • GENBANK/DQ103594
  • GENBANK/DQ493648
  • GENBANK/GU057342
  • GENBANK/HQ637177
  • GENBANK/JX027061