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

Ruiz-Ruano, Francisco J., Navarro-Domínguez, Beatriz, Camacho, Juan Pedro M. and Garrido-Ramos, Manuel A. (2022) Transposable element landscapes illuminate past evolutionary events in the endangered fern Vandenboschia speciosa. Genome, 65 (2). pp. 95-103. ISSN 0831-2796

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Abstract

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.

Item Type: Article
Additional Information: Funding Information: This research was financed by the Spanish Ministerio de Economía y Competitividad and FEDER funds, grant: CGL20210-14856 (subprograma BOS). F.J. Ruiz-Ruano was supported by a Junta de Andalucía fellowship (Spain), a postdoctoral fellowship from Sven och Lilly Lawskis fond (Sweden), and a Marie Skłodowska-Curie Individual Fellowship grant agreement 875732 (EU). The Dirección General de Gestión del Medio Natural y Espacios Protegidos of the Consejería de Medio Ambiente y Ordenación del Territorio de la Junta de Andalucía authorized and facilitated the sampling of the material. We are highly indebted to Carmen Rodríguez Hiraldo and Jaime Pereña Ortiz, who, together with the team of Agentes de Medio Ambiente of the Consejería, helped us with the sampling procedure.
Uncontrolled Keywords: climate crisis,demographic changes,endangered species,ferns,genome size,relict populations,tetraploidy,transposable elements,vandenboschia speciosa,biotechnology,molecular biology,genetics ,/dk/atira/pure/subjectarea/asjc/1300/1305
Faculty \ School: Faculty of Science > School of Biological Sciences
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Depositing User: LivePure Connector
Date Deposited: 11 Nov 2021 02:14
Last Modified: 24 May 2022 14:38
URI: https://ueaeprints.uea.ac.uk/id/eprint/82045
DOI: 10.1139/gen-2021-0022

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