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Analysis of transposons and repeat composition of the sunflower (Helianthus annuus L.) genome

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Abstract

A sample-sequencing strategy combined with slot–blot hybridization and FISH was used to study the composition of the repetitive component of the sunflower genome. One thousand six hundred thirty-eight sequences for a total of 954,517 bp were analyzed. The fraction of sequences that can be classified as repetitive using computational and hybridization approaches amounts to 62% in total. Almost two thirds remain as yet uncharacterized in nature. Of those characterized, most belong to the gypsy superfamily of LTR-retrotransposons. Unlike in other species, where single families can account for large fractions of the genome, it appears that no transposon family has been amplified to very high levels in sunflower. All other known classes of transposable elements were also found. One family of unknown nature (contig 61) was the most repeated in the sunflower genome. The evolution of the repetitive component in the Helianthus genus and in other Asteraceae was studied by comparative analysis of the hybridization of total genomic DNAs from these species to the sunflower small-insert library and compared to gene-based phylogeny. Very little similarity is observed between Helianthus species and two related Asteraceae species outside of the genus. Most repetitive elements are similar in annual and perennial Helianthus species indicating that sequence amplification largely predates such divergence. Gypsy-like elements are more represented in the annuals than in the perennials, while copia-like elements are similarly represented, attesting a different amplification history of the two superfamilies of LTR-retrotransposons in the Helianthus genus.

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Acknowledgments

This work was supported by PRIN-MIUR, Projects “Caratterizzazione della componente ripetitiva di genomi complessi in specie vegetali: modelli per angiosperme e gimnosperme” and “Variabilità di sequenza ed eterosi in piante coltivate”.

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Authors and Affiliations

  1. Genetics Section, Department of Crop Plant Biology, University of Pisa, Pisa, Italy

    Andrea Cavallini, Lucia Natali, Tommaso Giordani & Veronica Ferrillo

  2. Department of Crop and Environmental Sciences, University of Udine, Viale delle Scienze 208, 33100, Udine, Italy

    Andrea Zuccolo & Michele Morgante

  3. Istituto di Genomica Applicata, Parco Scientifico e Tecnologico Luigi Danieli, Udine, Italy

    Irena Jurman, Federica Cattonaro & Michele Morgante

  4. Department of Mathematics and Informatics, University of Udine, Udine, Italy

    Nicola Vitacolonna

  5. Department of Cellular and Environmental Biology, University of Perugia, Perugia, Italy

    Vania Sarri, Marilena Ceccarelli & Pier Giorgio Cionini

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  1. Andrea Cavallini
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  2. Lucia Natali
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  3. Andrea Zuccolo
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  11. Pier Giorgio Cionini
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Correspondence to Michele Morgante.

Additional information

Communicated by A. Bervillé.

Sequences from Helianthus annuus randomly sheared genomic DNA library and sequences of genes used for phylogenetic analyses are available at the URL: https://services.appliedgenomics.org/sequences-export/26-Helianthus/.

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Cavallini, A., Natali, L., Zuccolo, A. et al. Analysis of transposons and repeat composition of the sunflower (Helianthus annuus L.) genome. Theor Appl Genet 120, 491–508 (2010). https://doi.org/10.1007/s00122-009-1170-7

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  • DOI: https://doi.org/10.1007/s00122-009-1170-7

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