title: Efficient screening of long terminal repeat retrotransposons that show high insertion polymorphism via high-throughput sequencing of the primer binding site.
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.
authors: a Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushimanaka Kitaku, Okayama, Okayama 700-8530, Japan.
authors: Yuki
authors: Y
authors: Monden
authors: Nobuyuki
authors: N
authors: Fujii
authors: Kentaro
authors: K
authors: Yamaguchi
authors: Kazuho
authors: K
authors: Ikeo
authors: Yoshiko
authors: Y
authors: Nakazawa
authors: Takamitsu
authors: T
authors: Waki
authors: Keita
authors: K
authors: Hirashima
authors: Yosuke
authors: Y
authors: Uchimura
authors: Makoto
authors: M
authors: Tahara
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D017931:DNA Primers / Q000378:metabolism*; D018744:DNA, Plant / Q000235:genetics / Q000378:metabolism; D031985:Fragaria / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D016254:Mutagenesis, Insertional; D011110:Polymorphism, Genetic; D018626:Retroelements / Q000235:genetics*; D020079:Terminal Repeat Sequences
chemical_list: D017931:DNA Primers; D018744:DNA, Plant; D018626:Retroelements
keywords: high-throughput sequencing; marqueurs moléculaires; molecular markers; polymorphism; polymorphisme; primer binding site; retrotransposon; rétrotransposons; site d’appariement de l’amorce; séquençage à haut débit