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Open Access Research article

Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements

Minkyu Park12, SungHwan Jo34, Jin-Kyung Kwon25, Jongsun Park1678, Jong Hwa Ahn25, Seungill Kim12, Yong-Hwan Lee678, Tae-Jin Yang25, Cheol-Goo Hur4, Byoung-Cheorl Kang25, Byung-Dong Kim25 and Doil Choi25*

  • * Corresponding author: Doil Choi

  • † Equal contributors

Author Affiliations

1 Interdisciplinary Program in Agriculture Biotechnology, Seoul National University, Seoul 151-921, Korea

2 Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea

3 Seeders Inc., Daejeon, Korea

4 Bioinformatics Research Center, KRIBB, Daejeon, 305-806, Korea

5 Department of Plant Science, Seoul National University, Seoul, 151-921, Korea

6 Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea

7 Center for Fungal Pathogenesis, Seoul National University, Seoul 151-921, Korea

8 Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea

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BMC Genomics 2011, 12:85  doi:10.1186/1471-2164-12-85

Published: 29 January 2011



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.


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.


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.