Transposable element landscapes illuminate past evolutionary events in the endangered fern Vandenboschia speciosa Ruiz-Ruano Campaña, Francisco Jesús Navarro Domínguez, Beatriz María Martínez Camacho, Juan Pedro Garrido Ramos, Manuel Ángel Climate crisis Demographic changes Endangered species Ferns Genome size Relict populations Tetraploidy Transposable elements Vandenboschia speciosa This research was financed by the Spanish Ministerio de Economia y Competitividad and FEDER funds, grant: CGL20210-14856 (subprograma BOS). F.J. Ruiz-Ruano was supported by a Junta de Andalucia fellowship (Spain), a postdoctoral fellowship from Sven och Lilly Lawskis fond (Sweden), and a Marie Sklodowska-Curie Individual Fellowship grant agreement 875732 (EU). The Direccion General de Gestion del Medio Natural y Espacios Protegidos of the Consejeria de Medio Ambiente y Ordenacion del Territorio de la Junta de Andalucia authorized and facilitated the sampling of the material. We are highly indebted to Carmen Rodriguez Hiraldo and Jaime Perena Ortiz, who, together with the team of Agentes de Medio Ambiente of the Consejeria, helped us with the sampling procedure. 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 analyzed the transposable elements (TEs) and found that they comprise approximately 76% of the V. speciosa genome, thus being the most abundant type of DNA sequence in this gigantic genome. The 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, which 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 for the identification of almost half of them, which were most likely diverged sequence variants of the annotated TEs. In general, the TE composition in V. speciosa resembles the TE composition in seed plants. In addition, repeat landscapes revealed three episodes of amplification for all TEs, most likely due to demographic changes associated with past climate crises. 2022-02-21T11:54:14Z 2022-02-21T11:54:14Z 2021-09-18 journal article Published version: Francisco J. Ruiz-Ruano... [et al.]. Transposable element landscapes illuminate past evolutionary events in the endangered fern Vandenboschia speciosa. Genome. 65(2): 95-103. [https://doi.org/10.1139/gen-2021-0022] http://hdl.handle.net/10481/72925 eng info:eu-repo/grantAgreement/EC/H2020/875732 http://creativecommons.org/licenses/by-nc-nd/3.0/es/ open access Atribución-NoComercial-SinDerivadas 3.0 España Canadian Science Publishing