Efficient screening of long terminal repeat retrotransposons that show high insertion polymorphism via high-throughput sequencing of the primer binding site

Yuki Monden, Nobuyuki Fujii, Kentaro Yamaguchi, Kazuho Ikeo, Yoshiko Nakazawa, Takamitsu Waki, Keita Hirashima, Yosuke Uchimura, Makoto Tahara

Research output: Contribution to journalArticle

11 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)245-252
Number of pages8
JournalGenome
Volume57
Issue number5
DOIs
Publication statusPublished - Nov 13 2014

Keywords

  • High-throughput sequencing
  • Molecular markers
  • Polymorphism
  • Primer binding site
  • Retrotransposon

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology
  • Genetics

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