A new gypsy-like retroelement family in <i>Vitis vinifera</i>

Abstract

As a major part of most plant genomes, retrotransposons are distributed throughout the plant genome ubiquitously with high copy number and extensive heterogeneity. Various retrotransposon families with distinct structures differ in their distribution and roles among divergent plant species, due to unforeseen transposition activities.
We had performed in silico analysis of the Vitis vinifera 'Pinot Noir' genome to search for gypsy type retroelements homologues to the one identified in Pinus radiata (IFG7) and P. pinaster (PpRT1) and in Quercus suber (Corky). We intended to see the existence and structure of gypsy-like retroelements homologues in the Vitis genome as well as the existence of integration site preference. From all data and to perform a deeper analysis we chose 36 complete sequences copies in the Vitis genome. We used three genetic distance corrections, additional to p-distance to estimate retroelements insertion time and reverse transcriptase, integrase and LTR (Long Terminal Repeat) sequences to establish a phylogeny and to see the contributions of different regions according to the evolutionary rates. We found three elements with identical LTRs and two old elements that revealed recent and very old insertions as well as insertions inside other retroelements. Additionally, we found no preference for the integration site as shown by the different target site repeat for each element.