Characterization of various repetitive elements in pepper (Capsicum annuum)

Previous experiments show that repetitive DNA makes up a large fraction of the pepper genome and contributes to its three-fold size difference with tomato. Further isolation and characterization of repetitive DNA is needed to achieve a better understanding of pepper�s genetic makeup and the evolution of the Solanaceae genome. A random genomic library was constructed from mechanically sheared pepper DNA. Twenty-seven clones, containing anywhere from 200 to 3000 bp, were sequenced and then were analyzed using BLAST against the DNA sequence databases GenBank, TIGR, and SGN. Sequencing results indicate that over half of the clones matched a repetitive class in at least one database and include a variety of retrotransposon, centromeric, telomeric, and ribosomal sequences. Internal repeat structure was analyzed using MEME and demonstrates that pepper nuclear DNA is made up of many short, interspersed repetitive elements as well as some longer repeats with known function. PCR results indicate that some of these repetitive sub-classes occur in other taxa within the Solanaceae family and beyond.