Isolation of Ty1-copia-like Retrotransposon Sequences from the Apple Genome by Chromosome Walking Based on Modified SiteFinding-polymerase Chain Reaction

Authors: ZHAO, Guiling; ZHANG, Zhihong1; SUN, Haiyue1; LI, He1; DAI, Hongyan

Source: Acta Biochimica et Biophysica Sinica, Volume 39, Number 9, September 2007 , pp. 675-683(9)

Publisher: Blackwell Publishing

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Abstract:

Long terminal repeat (LTR) retrotransposons are powerful tools for studying genetic biodiversity, genome evolution, gene mutation, gene cloning and gene expression. The scarcity of retrotransposon sequence information restricts the development of these studies in higher plants. In the present study, 31 reverse transcriptase (RT) genes of Ty1-copia-like retrotransposons were identified from the apple genome by amplifying the RT coding region using degenerate primers. Nineteen RT genes showed extreme heterogeneity in terms of fragment size, base pair composition and open reading frame integrality. Originating from one 266 bp cloned RT gene, a 1966 bp Ty1-copia-like retrotransposon (named Tcrm1), including RT-ribonuclease H-LTR domain sequences, was achieved by chromosome walking based on modified SiteFinding-polymerase chain reaction. The comparison between Tcrm1 and other LTR retrotransposons in gene structure and sequence homology shows that Tcrm1 is the first Ty1-copia-like retrotransposon including an LTR domain in the apple genome. Dot blot analysis revealed that Tcrm1 copy number in the apple was approximately 1 × 103 copies per haploid genome.

Keywords: Malus domestica; Ty1-copia-like retrotransposon; long terminal repeat sequence; modified SiteFinding-polymerase chain reaction

Document Type: Research article

DOI: 10.1111/j.1745-7270.2007.00328.x

Affiliations: 1: College of Horticulture, Shenyang Agricultural University, Shenyang 110161, China

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