Identification and Characterization of Novel Gypsy-Type Retrotransposons in a Biodiesel Crop, Jatropha curcas L

Gypsy-type retrotransposons comprise a large proportion of the plant genome. Identification and determination of their chromosomal distribution could contribute to a better understanding of the role and dynamics behind the repetitive elements in the genome and karyotype. It would also facilitate the selection of retrotransposon families for informative DNA markers. In the present study, we applied a PCR method by using degenerate oligonucleotide primers to isolate the reverse transcriptase (RT) region of gypsy-type retrotransposons in Jatropha curcas L., a biofuel crop. The analysis of 50 isolated PCR-amplified fragments showed a range of heterogeneity among predicted amino acid sequences. Comparative phylogenetic analyses of isolated RT fragments together with retrotransposon families from other plants allowed us to identify three families (Jg1–3) of gypsy-type retroelements in the jatropha genome. Jg1 and Jg2, having primer binding sites (PBS) complementary to tRNAArg, were found as jatropha-specific and belonged to the same lineage, which suggests that they arose during early evolution. On the other hand, Jg3 of a different lineage included elements of other species and had PBS complementary to tRNAMet. The computer-based data mining of jatropha whole genome allowed us to identify a high-copy number gypsy-type family Jg4 of the same lineage as Jg1 and Jg2 which had PBS complementary to tRNAArg. Furthermore, fluorescence in situ hybridization (FISH) analysis demonstrated that these gypsy-type elements are located in the pericentromeric region of jatropha chromosomes. The data are discussed within the context of the distinct dynamics of the gypsy-type retrotransposon families, their evolution, and their value for phylogenetic and biodiversity studies.