Representational difference analysis reveals genomic differences between Q-robur and Q-suber: implications for the study of genome evolution in the genus Quercus

Very similar genome sizes, similar karyotypes and heterochromatin organisat ion, and identical number/position of ribosomal loci characterise the commo n oak (Q. robur) and the cork oak (Q. suber), two distantly related oak spe cies. Representational Difference Analysis (RDA) tvas used to subtract the genome of Q. suber from the genome of Q. robur in order to search for genom e differentiation. A library of 400 clones (bearing RDA fragments) represen ting genome differences between the two species was obtained. Seven Q. robu r-specific DNA sequences were analysed with respect to their molecular and chromosome organisation. All belong to the dispersed repetitive component o f the genome, as revealed by Southern hybridisation and in situ hybridisati on. They are present in the Q. robur genome in between 100 and 700 copies, and are distributed along the length of almost all chromosomes. A search fo r homologies between RDA fragments and sequences in Genbank revealed simila rities of all RDA fragments with known retrotransposons. The RDA fragments were also tested for their presence/absence in the genomes of six additiona l oak species belonging to different phylogenetic groups, in order to exami ne the evolutionary dynamics of these DNA sequences.