| Summary: | <p>Abstract</p> <p>Background</p> <p>Among the <it>Solanaceae </it>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.</p> <p>Results</p> <p>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 <it>Ty3/Gypsy</it>-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.</p> <p>Conclusions</p> <p>Compared to tomato pepper euchromatin doubled its size by differential accumulation of a specific group of <it>Ty3/Gypsy</it>-like elements. Our results could provide an insight on the mechanism of genome evolution in the <it>Solanaceae </it>family.</p>
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