Pararetrovirus-like sequences in the genome of plants

Primers were designed to reveal pararetrovirus-like sequences from potato (Solanum tuberosum) by PCR. One primer pair covered an area of the reverse transcriptase region, others covered the end of a transactivator and a repetitive region. The sequences obtained ranged from 800 to 1100 bp and had homology to known sequences of TPV (tobacco pararetrovirus) and TVCV (Tobacco vein clearing virus). Aligning the sequences from the potato genome gave a phylogenetic clustering into three different groups. Genomic Southern hybridization was used to confirm the results, with probes hybridizing to the full length of the digested DNA. In situ hybridization was used to localize different pararetrovirus-like sequences to the chromosomes of potato, which showed a low copy number sequence dispersed throughout the genome.;A diverse range of plant species was analysed with the pararetrovirus-like primers, and clones homologous to TPV and TVCV were obtained from a liverwort, a fern, tomato, tobacco, pea, rice and banana. These results were confirmed with genomic Southern hybridization, which also revealed pararetrovirus-like sequences in the DNA of other lower plants, Gymnosperms and Angiosperms.;Integrated pararetroviruses have been found to be a serious problem in banana breeding as micro-propagation may give rise to episomal viruses, reducing the yield considerably. The possibility of the widespread presence of pararetrovirus-like sequences in plants may have important implications for virus resistance, sudden pathogen outbreak and genomic evolution.