title: Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements.
abstract: 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.
authors.affiliation: Interdisciplinary Program in Agriculture Biotechnology, Seoul National University, Seoul 151-921, Korea.
authors.forename: Minkyu
authors.initials: M
authors.lastname: Park
authors.forename: SungHwan
authors.initials: S
authors.lastname: Jo
authors.forename: Jin-Kyung
authors.initials: JK
authors.lastname: Kwon
authors.forename: Jongsun
authors.initials: J
authors.lastname: Park
authors.forename: Jong Hwa
authors.initials: JH
authors.lastname: Ahn
authors.forename: Seungill
authors.initials: S
authors.lastname: Kim
authors.forename: Yong-Hwan
authors.initials: YH
authors.lastname: Lee
authors.forename: Tae-Jin
authors.initials: TJ
authors.lastname: Yang
authors.forename: Cheol-Goo
authors.initials: CG
authors.lastname: Hur
authors.forename: Byoung-Cheorl
authors.initials: BC
authors.lastname: Kang
authors.forename: Byung-Dong
authors.initials: BD
authors.lastname: Kim
authors.forename: Doil
authors.initials: D
authors.lastname: Choi
mesh_terms: D022041:Euchromatin / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D006570:Heterochromatin / Q000235:genetics; D017404:In Situ Hybridization, Fluorescence; D018551:Solanum lycopersicum / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D031701:Piper / Q000145:classification / Q000235:genetics*; D018626:Retroelements / Q000235:genetics; D020079:Terminal Repeat Sequences / Q000235:genetics
chemical_list: D022041:Euchromatin; D006570:Heterochromatin; D018626:Retroelements