Characterisation of copia-like retrotransposons in oil palm (Elaeis guineensis Jacq.)

The work aimed to isolate and characterise copia-like sequences from Elaeis guineensis. Thirty-two different RT (reverse transcriptase) sequences were isolated from a single oil palm genome using degenerate primers. Extreme sequence heterogeneity was observed. The DNA and protein sequences were assigned to three different classes (A, B, Q on the basis of bootstrapping. We estimated the copy number of the three different classes by using a dot-blot analysis. The comparative results suggest that class-B RT sequences occur at a higher copy number in Cocos nucifera than in Elaeis guineensis and E. oleifera. Class-C RT sequences, which comprise the bulk of isolated sequences, occur in much higher copy number in Elaeis guineensis than in Cocos nucifera, and E. oleifera. Class-A sequences, which have low copy number in Elaeis guineensis and Cocos nucifera, are not present in E. oleifera. Our preliminary results suggest that class-C sequences represent about 5% of the E. guineensis genome, class B, 1% and class A, 0.1%. The methylation status of genomic domains specified by the RT probes was analysed using two pairs of restriction enzymes, each pair having the same recognition sites but different methylation sensitivities (MspI, HpaII and Sau3AI, MboI). Results from these experiments showed clearly that the genomic domains specified by the RT probes are methylated. These also suggest that a higher copy number appears to correlate to a higher degree of methylation. Our preliminary results suggest that copia-like retrotransposons, because of their ubiquity and diversity, have great potential as genetic markers for plant genome and biodiversity analysis in E. guineensis.