BACKGROUND: Among the Solanaceae plants, the pepper genome is three times larger 
than that of tomato. Although the gene repertoire and gene order of both species 
are well conserved, the cause of the genome-size difference is not known. To 
determine the causes for the expansion of pepper euchromatic regions, we 
compared the pepper genome to that of tomato.
RESULTS: For sequence-level analysis, we generated 35.6 Mb of pepper genomic 
sequences from euchromatin enriched 1,245 pepper BAC clones. The comparative 
analysis of orthologous gene-rich regions between both species revealed 
insertion of transposons exclusively in the pepper sequences, maintaining the 
gene order and content. The most common type of the transposon found was the LTR 
retrotransposon. Phylogenetic comparison of the LTR retrotransposons revealed 
that two groups of Ty3/Gypsy-like elements (Tat and Athila) were overly 
accumulated in the pepper genome. The FISH analysis of the pepper Tat elements 
showed a random distribution in heterochromatic and euchromatic regions, whereas 
the tomato Tat elements showed heterochromatin-preferential accumulation.
CONCLUSIONS: Compared to tomato pepper euchromatin doubled its size by 
differential accumulation of a specific group of Ty3/Gypsy-like elements. Our 
results could provide an insight on the mechanism of genome evolution in the 
Solanaceae family.