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

Cited 24 time in Web of Science Cited 23 time in Scopus
Authors
Park, Minkyu; Jo, SungHwan; Kwon, Jin-Kyung; Park, Jongsun; Ahn, Jong Hwa; Kim, Seungill; Lee, Yong-Hwan; Yang, Tae-Jin; Hur, Cheol-Goo; Kang, Byoung-Cheorl; Kim, Byung-Dong; Choi, Doil
Issue Date
2011-01-29
Publisher
BioMed Central
Citation
BMC Genomics, 12(1):85
Description
This is an Open Access article distributed under the terms of the Creative Commons
Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in
any medium, provided the original work is properly cited.
Abstract
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.
Language
English
URI
https://hdl.handle.net/10371/100467
DOI
https://doi.org/10.1186/1471-2164-12-85
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College of Agriculture and Life Sciences (농업생명과학대학)Program in Agricultural Biotechnology (협동과정-농업생물공학전공)Journal Papers (저널논문_협동과정-농업생물공학전공)
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