Abnormal LTR retrotransposons formed by the recombination outside the host genome

Long terminal repeat (LTR) retrotransposons are the dominant feature of higher plant genomes, which have a similar life cycle with retrovirus. Previous studies cannot account for all observed complex LTR retrotransposon patterns. In this study, we first identified 63 complex LTR retrotransposons in...

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Bibliographic Details
Published inbioRxiv
Main Authors Zeng, Fanchun, Sun, Zhongyi
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 25.10.2018
Subjects
Genomes
Homologous recombination
Integration
Life cycles
Long terminal repeat
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Summary:Long terminal repeat (LTR) retrotransposons are the dominant feature of higher plant genomes, which have a similar life cycle with retrovirus. Previous studies cannot account for all observed complex LTR retrotransposon patterns. In this study, we first identified 63 complex LTR retrotransposons in rice genome, and most of complex elements harbored flanking target-site duplications (TSDs). But these complex elements in which outermost LTRs had not the most highly homologous can t be explained. We propose a new model that the homologous recombination of two new different normal LTR retrotransposon elements in the same family can occur before their integration to the rice genome. The model can explain at least fourteen complex retrotransposons formations. We also find that normal LTR retrotransposons can swap their LTRs to generate abnormal LTR retrotransposons in which LTRs are different because of homologous recombination before their integration to the genome.
DOI:10.1101/452573