TY - JOUR
T1 - Efficient screening of long terminal repeat retrotransposons that show high insertion polymorphism via high-throughput sequencing of the primer binding site
AU - Monden, Yuki
AU - Fujii, Nobuyuki
AU - Yamaguchi, Kentaro
AU - Ikeo, Kazuho
AU - Nakazawa, Yoshiko
AU - Waki, Takamitsu
AU - Hirashima, Keita
AU - Uchimura, Yosuke
AU - Tahara, Makoto
PY - 2014/11/13
Y1 - 2014/11/13
N2 - 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.
AB - 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.
KW - High-throughput sequencing
KW - Molecular markers
KW - Polymorphism
KW - Primer binding site
KW - Retrotransposon
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UR - http://www.scopus.com/inward/citedby.url?scp=84909641057&partnerID=8YFLogxK
U2 - 10.1139/gen-2014-0031
DO - 10.1139/gen-2014-0031
M3 - Article
C2 - 25072847
AN - SCOPUS:84909641057
VL - 57
SP - 245
EP - 252
JO - Genome / National Research Council Canada = Genome / Conseil national de recherches Canada
JF - Genome / National Research Council Canada = Genome / Conseil national de recherches Canada
SN - 0831-2796
IS - 5
ER -