Diversity in the integrase coding domain of a gypsy-like retrotransposon among wild relatives of rice in the Oryza officinalis complex

The Oryza officinalis complex is a genetically diverse, tertiary genepool o f rice. We analyzed part of the primary structure of the integrase coding d omain (ICD) of a gypsy-like retrotransposon from species of the O. officina lis species complex. PCR was performed with degenerate primers that hybridi zed to conserved sequences in the integrase genes of gypsy-type retrotransp osons, using total DNA from different species of the O. officinalis complex as templates. Cloning and sequencing of the PCR products showed that the a mplified fragments are highly homologous to each other (75-90%) and belong to one family of retrotransposons that is related to the previously studied RIRE-2 element from rice. Two main subfamilies of 292 and 351 bp were dist inguished. Analysis of primary sequence data supports previous reports that sequence divergence during vertical transmission has been the major influe nce on the evolution of gypsy-type retrotransposons in Oryza species. Based on sequence data phylogenetic relationships among species of the O. offici nalis complex were estimated. The data suggests that O. eichingeri is more closely related to the ancestral species of the complex.