Genomic Structure and Evolution of the Citrus Tristeza Virus (CTV) Resistance Locus in Poncirus and Citrus

Citrus tristeza virus (CTV) is a major viral pathogen causing several diseases to citrus; the Ctv locus in Poncirus trifoliata, a close relative of citrus, confers resistance to multiple isolates of CTV. To facilitate further understanding of the gene content and genomic structure of the Ctv locus, we developed bacterial artificial chromosome (BAC) contigs to encompass two haplotypes of the gene region and assembled a 278-kb sequence of the Ctv region in Poncirus and a 253-kb sequence of the ctv region in Citrus grandis. We further retrieved the sequences from the Citrus clementine and Citrus sinensis genome databases corresponding to the ctv region of C. grandis. Comparative analysis of the genomic sequences of the four homologous regions revealed considerable variation in resistance-gene (R-gene) copy number and localization from species to species. Strong conservation was observed in three genes located at both sides of the locus while wide divergence was seen in genes located at the center of this locus. Dramatic structural rearrangements had occurred, resulting in an expansion of ~60 kb at the Ctv region over the ctv regions. The center of the Ctv region is packed with a rich and diverse group of retrotransposable elements (REs), while the ctv regions are essentially free of REs. These data suggest that REs have played a major role in the expansion and diversification of the Ctv locus.