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Genome-wide analysis of LTR-retrotransposon expression in leaves of Populus × canadensis water-deprived plants

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Abstract

Retrotransposons represent a major component of plant genomes; however, large-scale studies on their expression are rare. Massively parallel sequencing offers new analytical possibilities enabling a comprehensive study of retrotransposon RNA transcription. We evaluated the expression of long terminal repeat-retrotransposons in leaves of two sister hybrids Populus × canadensis (P. deltoides × P. nigra), subjected to moderate or severe water deprivation by mapping Illumina RNA-Seq reads onto a set of 958 unique full-length retrotransposons of P. trichocarpa. Detectable levels of transcription were ascertained for 140 retrotransposons in 1 hybrid and 182 in the other. The two hybrids showed different retrotransposon expression levels, and these differences reduced at increasing drought levels. The number of expressed Gypsy elements in control and water-deprived plants was higher than those of Copia, as were their expression levels. The two hybrids showed different retrotransposon expression patterns following water deprivation. Such variations between hybrids were related to differential expression of a few genes involved in chromatin methylation and remodeling. Overall, our data indicate that even in genetically close individuals, large differences can occur in retrotransposon expression, with possible consequences for genome differentiation.

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Abbreviations

RE:

Retrotransposon

LTR-RE:

Long terminal repeat-retrotransposon

RPKM:

Reads per kilobase per million reads mapped

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Acknowledgments

This research work was supported by PRIN-MIUR, Italy, project “Verso la delucidazione delle basi molecolari dell’eterosi nelle piante coltivate: variazione cis-regolatoria ed espressione genica in ibridi di pioppo” and, in part, by European Community’s Seventh Framework Program (FP7/2007-2013), under grant agreement number 211917 (ENERGYPOPLAR).

Thanks are due to Dr. Catherine Bastien (INRA-UAGPF, Orleans, France) for providing the hybrid plants, to Pierfrancesco Miscali (DiSAAA-a, Pisa, Italy) for technical collaboration on data handling and treatment, and to Dr. John A. Walsh (Warwick University, UK) for critical reading of the manuscript.

Data archiving statement

All LTR-RE sequences are available in the Department of Agriculture, Food, and Environment of the University of Pisa repository website (http://www.agr.unipi.it/ricerca/plant-genetics-and-genomics-lab/sequencerepository.html).

All genomic DNA and cDNA raw Illumina sequences used in this work are available at the NCBI Sequence Read Archive under the accession numbers SRP078030 (submission: Hybrid Populus deltoides × Populus nigra Raw sequence reads) and SRP024267 (submission: Populus × canadensis RNAseq).

The global analysis of LTR-RE and gene expression is available in an excel file in the Department of Agriculture, Food, and Environment of University of Pisa repository website (http://www.agr.unipi.it/Sequence-Repository.358.0.html), in which each LTR-RE and each gene were represented by its absolute expression level in control, moderately dehydrated and severely dehydrated leaves.

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Authors and Affiliations

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

    Tommaso Giordani, Rosa Maria Cossu, Flavia Mascagni, Andrea Cavallini & Lucia Natali

  2. School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK

    Rosa Maria Cossu

  3. Institute of Applied Genomics, Udine, Italy

    Fabio Marroni & Michele Morgante

  4. Department of Crop and Environmental Sciences, University of Udine, Udine, Italy

    Fabio Marroni & Michele Morgante

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  1. Tommaso Giordani
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  2. Rosa Maria Cossu
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  4. Fabio Marroni
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  5. Michele Morgante
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  6. Andrea Cavallini
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  7. Lucia Natali
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Corresponding author

Correspondence to Lucia Natali.

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Communicated by A. Brunner

Tommaso Giordani and Rosa Maria Cossu contributed equally to this work.

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Giordani, T., Cossu, R.M., Mascagni, F. et al. Genome-wide analysis of LTR-retrotransposon expression in leaves of Populus × canadensis water-deprived plants. Tree Genetics & Genomes 12, 75 (2016). https://doi.org/10.1007/s11295-016-1036-5

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