The distribution and organization of Ty1-copia-like retrotransposable elements in the genome of Vigna unguiculata (L.) Walp. (Cowpea) and its relatives

Abstract

Ty1-copia-like retrotransposable elements were amplified from Vigna species by the polymerase chain reaction (PCR) with primers derived from the conserved region of the reverse transcriptase (RT) gene. Southern blots of genomic DNA digests from Vigna unguiculata and related species probed with the PCR derived sequences from V. unguiculata (rt-cow), V. unguiculata subsp. dekindtiana (rt-dek), V. luteola (rt-lut) and V. vexillata (rt-vex) showed variable hybridization patterns and intensities, generally correlating with taxonomic relationships. Sequencing of four clones revealed homologies to the reverse transcriptase gene of known Ty1-copia-like elements, although comparison of the predicted peptide sequences with each other and previously isolated reverse transcriptase genes from other legumes typically showed less than 50% identity. Fluorescence in situ hybridization of the PCR products showed that Ty1-copia elements represented a major fraction of the genome and were dispersed relatively uniformly over all chromosomes, with exclusion from centromeric, subtelomeric and nucleolar organizing regions, and a few sites of greater abundance. We are now able to start to understand the organization, variability and evolution of retrotransposons within the Fabaceae.