Transposable element landscapes illuminate past evolutionary events in the endangered fern Vandenboschia speciosa

Francisco J. Ruiz-Ruano, Beatriz Navarro-Domínguez, Juan Pedro M. Camacho, Manuel A. Garrido-Ramos

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3 Citations (Scopus)
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Vandenboschia speciosa is an endangered tetraploid fern species with a large genome (10.5 Gb). Its geographical distribution is characterized by disjoined tertiary flora refuges, with relict populations that survived past climate crises. Here we analyze the transposable elements (TEs) and found that they comprise about 76% of the V. speciosa genome, thus being the most abundant kind of DNA sequences in this gigantic genome. V. speciosa genome is composed of 51% and 5.6% of Class I and Class II elements, respectively. LTR retrotransposons were the most abundant TEs in this species (at least 42% of the genome), followed by non-LTR retrotransposons that constituted at least 8.7% of the genome of this species. We introduce an additional analysis to identify the nature of non-annotated elements (19% of the genome). A BLAST search of the non-annotated contigs against the V. speciosa TE database allowed determining the identity of almost half of them, which were most likely diverged sequence variants of the annotated TEs. In general, TE composition in V. speciosa resembles TE composition in seed plants. In addition, repeat landscapes revealed three episodes of amplification for all TEs, most likely due to demographic changes associated to past climate crises.
Original languageEnglish
Pages (from-to)95-103
Number of pages9
Issue number2
Early online date23 Sep 2021
Publication statusPublished - Feb 2022


  • Climate crisis
  • Demographic changes
  • Endangered species
  • Ferns
  • Genome size
  • Relict populations
  • Tetraploidy
  • Transposable elements
  • Vandenboschia speciosa

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