このエントリーをはてなブックマークに追加
ID 52815
FullText URL
Author
Fujii, Nobuyuki
Yamaguchi, Kentaro
Ikeo, Kazuho
Nakazawa, Yoshiko
Waki, Takamitsu
Hirashima, Keita
Uchimura, Yosuke
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.
Keywords
retrotransposon
primer binding site
high-throughput sequencing
polymorphism
molecular markers
Published Date
2014-06-25
Publication Title
Genome
Volume
volume57
Issue
issue5
Publisher
NRC Research Press
Start Page
245
End Page
252
Content Type
Journal Article
language
英語
File Version
author
Refereed
True
DOI