In silico Phylogenetic Analysis of Transposable Elements in Plants.

Transposable elements of the family exhibit a cross-kingdom distribution. The plant transposons are proposed to play a critical role in plant adaptive evolution and DNA damage repair. The sequencing of an increasing number of plant genomes has facilitated the discovery of a plethora of elements. This enabled us to perform an in-depth phylogenetic analysis of consensus sequences in the fully-sequenced genomes of 11 plant species that represent diverse taxonomic divisions. Four putative nucleotide sequences were detected in cottonwood that were similar to the corresponding animal elements, which are possibly sequence artifacts. Phylogenetic trees were constructed based both on the known and putative sequences, by employing two different methods of phylogenetic inference. On the basis of the reconstructed phylogeny, plant elements have rather evolved through kingdom-specific vertical gene transfer and gene amplifications within eudicotyledons, monocotyledons, and chlorophytes. Furthermore, the plant sequences were searched for conserved DNA and amino acid sequence features. In this way, diagnostic sequence patterns were detected which allowed us to assign functional annotations to the plant sequences.