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A computational genome-wide analysis of long terminal repeats retrotransposon expression in sunflower roots (Helianthus annuus L.)

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Abstract

Long terminal repeats (LTR) retrotransposons have a major role in determining genome size, structure and function, thanks to their ability to transpose. We performed a meta-analysis of LTR-retrotransposon expression in roots of sunflower plantlets treated with different plant hormones, chemicals and NaCl. By using Illumina cDNA libraries, available from public repositories, we measured the number of reads matching the retrotranscriptase domains isolated from a whole genome library of retrotransposons. LTR-retrotransposons resulted in general barely expressed, except for 4 elements, all belonging to the AleII lineage, which showed high transcription levels in roots of both control and treated plants. The expression of retrotransposons in treated plants was slightly higher than in the control. Transcribed elements belonged to specific chromosomal loci and were not abundant in the genome. A few elements resulted differentially expressed depending on the treatment. Results suggest that, although most retrotransposons are not expressed, the transcription of such elements is related to their abundance, to their position in the chromosome and to their lineage.

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Acknowledgements

This research was supported by the Department of Agriculture, Food and Environment of the University of Pisa, Italy, Project “Plantomics”.

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  1. Flavia Mascagni and Alberto Vangelisti have contributed equally to this work.

Authors and Affiliations

  1. Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy

    Flavia Mascagni, Alberto Vangelisti, Gabriele Usai, Tommaso Giordani, Andrea Cavallini & Lucia Natali

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  1. Flavia Mascagni
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  2. Alberto Vangelisti
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  3. Gabriele Usai
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  4. Tommaso Giordani
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  5. Andrea Cavallini
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Correspondence to Andrea Cavallini or Lucia Natali.

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Mascagni, F., Vangelisti, A., Usai, G. et al. A computational genome-wide analysis of long terminal repeats retrotransposon expression in sunflower roots (Helianthus annuus L.). Genetica 148, 13–23 (2020). https://doi.org/10.1007/s10709-020-00085-4

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