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LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species

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Abstract

LTR-retrotransposons are ubiquitous and highly abundant in plant genomes. Moreover, LTR-retrotransposons can often cause genome obesity in plants. Although Lilium species have been known carrying large genomes among flowering plants, reports on the LTR-retrotransposons in Lilium species are rather limited. We isolated a novel Ty3/gypsy-like retrotransposon, LIRE-del, and two Ty1/copia-like retrotransposons, a LIRE-del and an unclassified, from a fosmid clone of Lilium longiflorum. Decayed internal ORF sequences indicated that they were non-autonomous elements. IRAP protocol was developed based on the LTR sequences of the isolated LTR-retrotransposons. Fourteen primer combinations showed clear distinctive PCR amplification bands that were highly informative in the analysis of species relationship among Lilium species. The phylogenetic relationship based on the IRAP profile revealed some discordant with phylogenetic studies based on the ITS sequences of 45S ribosomal gene and matK gene variations in a few species. Thus, the phylogenetic relationship among Lilium species may need to be re-evaluated with other tools such as cross compatibility and selectively neutral genetic markers.

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Acknowledgments

This work was supported by a grant NRF-2013R1A1A2043773 from the Korea Research Foundation to NSK.

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The authors declare no conflict of interest on the contents of the manuscript.

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Authors and Affiliations

  1. Department of Molecular Bioscience, Kangwon National University, Chuncheon, 200-701, Korea

    Sung-Il Lee & Nam-Soo Kim

  2. Department of Horticulture, Kangwon National University, Chuncheon, Korea, 200-701

    Jong-Hwa Kim

  3. Department of Agricultural Life Science, Kangwon National University, Chuncheon, 200-701, Korea

    Kyong-Cheul Park

  4. Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, 200-701, Korea

    Nam-Soo Kim

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  1. Sung-Il Lee
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Correspondence to Nam-Soo Kim.

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Lee, SI., Kim, JH., Park, KC. et al. LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species. Genetica 143, 343–352 (2015). https://doi.org/10.1007/s10709-015-9833-6

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