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Retrotransposon distribution and copy number variation in gymnosperm genomes

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Abstract

Retrotransposable elements (REs) and related sequences form a large proportion of conifer genomes. During genome evolution, some RE sequences are degraded or eliminated, but some are evolutionarily stable, and can be identified even in distantly related species. Use of genome sequence information from loblolly pine (Pinus taeda) enables investigation of divergent non-coding RE sequences in other pine and conifer species, including Scots pine (Pinus sylvestris). Non-specific inter-retrotransposon amplified polymorphism technique (IRAP) as well as the amplification polymorphism of 12 RE families were investigated in 80 gymnosperm species. The obtained results were compared with phylogenetic relationships among gymnosperms. Investigation of distantly related gymnosperm species reveals persistent RE sequences, such as IFG and Pineywoods, distributed among a wide range of plant lineages. RE sequence divergence was observed, reflecting periods of inactivity and degradation during speciation of pine lineages, as demonstrated by the delineation of the main pine subgenera. Intraspecific variation of 10 RE copy numbers (CN) between Scots pine individuals ranged from 8.9 to 26.6% of the overall mean estimates. CN analyses were performed in 16 additional gymnosperm species. The analysed pine species contained a similar complement of RE families; however, CN and genome occupation proportions differ. A decrease in RE CN estimates can reflect sequence divergence, associated with independent transposition events. Transposition of some REs can be induced by stress conditions; therefore, even distantly related species inhabiting extreme environments could have similar patterns or distribution of these elements.

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Acknowledgements

This study was funded by the Latvian Council of Science project “Investigation of molecular defence mechanisms in Scots pine (Pinus sylvestris L.)” (Nr. 284/2012).

Data archiving statement

The nucleotide sequences obtained in this study have been submitted to the NCBI Genbank database (accession numbers KY865037-KY865093).

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Authors and Affiliations

  1. Genetic Resource Centre, Latvian State Forest Research Institute “Silava”, Rigas 111, Salaspils, LV-2169, Latvia

    Angelika Voronova, Viktorija Belevich, Anna Korica & Dainis Rungis

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  1. Angelika Voronova
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  2. Viktorija Belevich
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  3. Anna Korica
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  4. Dainis Rungis
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Correspondence to Angelika Voronova.

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Communicated by P. Ingvarsson

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Voronova, A., Belevich, V., Korica, A. et al. Retrotransposon distribution and copy number variation in gymnosperm genomes. Tree Genetics & Genomes 13, 88 (2017). https://doi.org/10.1007/s11295-017-1165-5

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  • DOI: https://doi.org/10.1007/s11295-017-1165-5

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