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Transposon Activity in Plant Genomes

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Plant Omics: Trends and Applications

Abstract

Transposable elements (TEs) were first discovered in maize plants. However, they exist in all plant species investigated so far. Although plants with small genomes have smaller transposon percentages, plants with large genomes have high transposon percentages. For example,Arabidopsis thaliana has a genome size of 125 Mb, which comprises 14 % transposons, and theHordeum vulgare genome (5300 Mb) has 80 %. TEs are classified into two major groups based on their transposition mechanism. Class I elements are characterized by DNA sequences with homology to reverse transcriptase, and they are often referred to as retroelements, retrotransposons, or retrovirus-like elements. Retrotransposons function by a copy-and-paste transposition mechanism. Class II TEs (DNA transposons) move by a cut-and-paste mechanism. TEs affect the genome dynamics of plants by regulation of gene expression and chromosomal mutations (such as duplications, insertions/deletions, and structural variations). Transposition rates among generations are about 10−3 to 10−4, which is a higher rate than spontaneous mutations. All TEs in a cell are named as transposomes, and transposomics is a new area to work with transposomes. Although some bioinformatics software has recently been developed for the annotation of TEs in sequenced genomes, there are very few computational tools strictly dedicated to the identification of active TEs using genome-wide approaches. In this review article, after a brief introduction and review of the transposable elements, we discuss the effects of TEs in plant gene expression and evolution, and also present our recent research data on barley retrotransposons.

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Acknowledgments

We are grateful to the Research Fund of Istanbul University for financial support (Projects 20212 and 20316).

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Correspondence to Nermin Gozukirmizi .

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Gozukirmizi, N., Temel, A., Marakli, S., Yilmaz, S. (2016). Transposon Activity in Plant Genomes. In: Hakeem, K., Tombuloğlu, H., Tombuloğlu, G. (eds) Plant Omics: Trends and Applications. Springer, Cham. https://doi.org/10.1007/978-3-319-31703-8_4

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