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Novel Transposable Elements in Solanaceae: Evolutionary Relationships among Tnt1-related Sequences in Wild Petunia Species

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Abstract

Transposable elements (TEs) are widespread in eukaryotic genomes. The diversity and abundance of TEs are highly variable among species and may correspond to particular relationships between a species and the elements in its genome. There are often many TE families within a single genome; thus, the amplification of one TE family may influence the amplification of other families. LTR retrotransposons (LTR-RTs) are extremely abundant in flowering plants, and Tnt1 is one of the most well known. First characterized in tobacco, Tnt1-related sequences have since been reported in other genera of Solanaceae. In this study, we investigated the profile of Tnt1-related sequences among the species of three Solanaceae genera through genomic amplification and the cloning of partial sequences. The analysis of these sequences revealed high levels of diversity and showed that the sequences are not as closely related to Tnt1 as had been previously hypothesized. The classification of the sequences yielded ten possible families of LTR-RTs, which are, in addition to Tnt1, all members of the Tork clade within the Copia superfamily. However, the sequences did not follow the phylogeny of the species and were not homogeneously distributed. One family includes only sequences of taxa that inhabit dry areas. These findings were consistent with previous suggestions of an early association of Tnt1-related elements with the evolution of several Solanaceae species.

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Acknowledgments

We thank the Associate Editor and three anonymous reviewers for their comments and suggestions, which have improved this manuscript. This project was supported by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq); the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), the Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (FAPERGS) and the Programa de Pós-Graduação em Genética e Biologia Molecular da Universidade Federal do Rio Grande do Sul (PPGBM-UFRGS).

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Authors and Affiliations

  1. Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Bento Gonçalves 9500, Po Box 15053, 91501-970, Porto Alegre, RS, Brazil

    Raquel A. Kriedt & Loreta B. Freitas

  2. GaTE Lab, Department of Botanics, Universidade de São Paulo, Rua do Matão 277, São Paulo, 05508-090, SP, Brazil

    Guilherme M. Q. Cruz

  3. Laboratory of Genomic and Molecular Biology, Pontifícia Universidade Católica do Rio Grande do Sul, Ipiranga 6681, 90610-001, Porto Alegre, RS, Brazil

    Sandro L. Bonatto

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  1. Raquel A. Kriedt
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  2. Guilherme M. Q. Cruz
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  3. Sandro L. Bonatto
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  4. Loreta B. Freitas
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Correspondence to Loreta B. Freitas.

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Kriedt, R.A., Cruz, G.M.Q., Bonatto, S.L. et al. Novel Transposable Elements in Solanaceae: Evolutionary Relationships among Tnt1-related Sequences in Wild Petunia Species. Plant Mol Biol Rep 32, 142–152 (2014). https://doi.org/10.1007/s11105-013-0626-8

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