Citrus and Prunus copia-like retrotransposons

Many of the world's most important citrus cultivars ("Washington Navel", sa tsumas, clementines) have arisen through somatic mutation. This phenomenon occurs fairly often in the various species and varieties of the genus. The presence of copia-like retrotransposons has been investigated in fruit tree s, especially citrus, by using a PCR assay designed to detect copia-like re verse transcriptase (RT) sequences. Amplification products from a genotype of each the following species Citrus sinensis, Citrus grandis, Citrus cleme ntina, Prunus armeniaca and Prunus amygdalus, were cloned and some of them sequenced. Southern-blot hybridization using RT clones as probes showed tha t multiple copies are integrated throughout the citrus genome, while only 1 -3 copies are detected in the P. armeniaca genome, which is in accordance w ith the Citrus and Prunus genome sizes. Sequence analysis of RT clones allo wed a search for homologous sequences within three gene banks. The most sim ilar ones correspond to RT domains of copia-like retrotransposons from unre lated plant species. Cluster analysis of these sequences has shown a great heterogeneity among RT domains cloned from the same genotype. This finding supports the hypothesis that horizontal transmission of retrotransposons ha s occurred in the past. The species presenting a RT sequence most similar t o citrus RT clones is Gnetum montanum, a gymnosperm whose distribution area coincides with two of the main centers of origin of Citrus spp. A new C-me thylated restriction DNA fragment containing a RT sequence is present in na vel sweet oranges, but not in Valencia oranges from which the former origin ated suggesting, that retrotransposon activity might be, at least in part, involved in the genetic variability among sweet orange cultivars. Given tha t retrotransposons are quite abundant throughout the citrus genome, their a ctivity should be investigated thoroughly before commercializing any transg enic citrus plant where the transgene(s) is part of a viral genome in order to avoid its possible recombination with an active retroelement. Focusing on other strategies to control virus diseases is recommended in citrus.