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ID 52815
フルテキストURL
著者
Monden, Yuki Graduate School of Environmental and Life Science, Okayama University
Fujii, Nobuyuki Center for Information Biology, National Institute of Genetics Research Organization of Information and Systems
Yamaguchi, Kentaro Graduate School of Environmental and Life Science, Okayama University
Ikeo, Kazuho Center for Information Biology, National Institute of Genetics Research Organization of Information and Systems
Nakazawa, Yoshiko Biotechology Division, Tochigi Prefectural Agricultural Experiment Station
Waki, Takamitsu Biotechology Division, Tochigi Prefectural Agricultural Experiment Station
Hirashima, Keita Department of Research Plan and Strategy, Fukuoka Agricultural Research Center
Uchimura, Yosuke Department of Research Plan and Strategy, Fukuoka Agricultural Research Center
Tahara, Makoto Graduate School of Environmental and Life Science, Okayama University
抄録
Retrotransposons have been used frequently for the development of molecular markers by using their insertion polymorphisms among cultivars, because multiple copies of these elements are dispersed throughout the genome and inserted copies are inherited genetically. Although a large number of long terminal repeat (LTR) retrotransposon families exist in the higher eukaryotic genomes, the identification of families that show high insertion polymorphism has been challenging. Here, we performed an efficient screening of these retrotransposon families using an Illumina HiSeq2000 sequencing platform with comprehensive LTR library construction based on the primer binding site (PBS), which is located adjacent to the 5′ LTR and has a motif that is universal and conserved among LTR retrotransposon families. The paired-end sequencing library of the fragments containing a large number of LTR sequences and their insertion sites was sequenced for seven strawberry (Fragaria × ananassa Duchesne) cultivars and one diploid wild species (Fragaria vesca L.). Among them, we screened 24 families with a “unique” insertion site that appeared only in one cultivar and not in any others, assuming that this type of insertion should have occurred quite recently. Finally, we confirmed experimentally the selected LTR families showed high insertion polymorphisms among closely related cultivars.
キーワード
retrotransposon
primer binding site
high-throughput sequencing
polymorphism
molecular markers
発行日
2014-06-25
出版物タイトル
Genome
57巻
5号
出版者
NRC Research Press
開始ページ
245
終了ページ
252
資料タイプ
学術雑誌論文
言語
English
OAI-PMH Set
岡山大学
論文のバージョン
author
査読
有り
DOI