start-ver=1.4
cd-journal=joma
no-vol=57
cd-vols=
no-issue=5
article-no=
start-page=245
end-page=252
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2014
dt-pub=20140625
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Efficient screening of long terminal repeat retrotransposons that show high insertion polymorphism via high-throughput sequencing of the primer binding site
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=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.
en-copyright=
kn-copyright=

en-aut-name=MondenYuki
en-aut-sei=Monden
en-aut-mei=Yuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=FujiiNobuyuki
en-aut-sei=Fujii
en-aut-mei=Nobuyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=YamaguchiKentaro
en-aut-sei=Yamaguchi
en-aut-mei=Kentaro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=IkeoKazuho
en-aut-sei=Ikeo
en-aut-mei=Kazuho
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=NakazawaYoshiko
en-aut-sei=Nakazawa
en-aut-mei=Yoshiko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

en-aut-name=WakiTakamitsu
en-aut-sei=Waki
en-aut-mei=Takamitsu
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=

en-aut-name=HirashimaKeita
en-aut-sei=Hirashima
en-aut-mei=Keita
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=

en-aut-name=UchimuraYosuke
en-aut-sei=Uchimura
en-aut-mei=Yosuke
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=

en-aut-name=TaharaMakoto
en-aut-sei=Tahara
en-aut-mei=Makoto
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=

affil-num=1
en-affil=
kn-affil=Graduate School of Environmental and Life Science, Okayama University

affil-num=2
en-affil=
kn-affil=Center for Information Biology, National Institute of Genetics Research Organization of Information and Systems

affil-num=3
en-affil=
kn-affil=Graduate School of Environmental and Life Science, Okayama University

affil-num=4
en-affil=
kn-affil=Center for Information Biology, National Institute of Genetics Research Organization of Information and Systems

affil-num=5
en-affil=
kn-affil=Biotechology Division, Tochigi Prefectural Agricultural Experiment Station

affil-num=6
en-affil=
kn-affil=Biotechology Division, Tochigi Prefectural Agricultural Experiment Station

affil-num=7
en-affil=
kn-affil=Department of Research Plan and Strategy, Fukuoka Agricultural Research Center

affil-num=8
en-affil=
kn-affil=Department of Research Plan and Strategy, Fukuoka Agricultural Research Center

affil-num=9
en-affil=
kn-affil=Graduate School of Environmental and Life Science, Okayama University
en-keyword=retrotransposon
kn-keyword=retrotransposon
en-keyword=primer binding site
kn-keyword=primer binding site
en-keyword=high-throughput sequencing
kn-keyword=high-throughput sequencing
en-keyword=polymorphism
kn-keyword=polymorphism
en-keyword=molecular markers
kn-keyword=molecular markers
END