Transposable element landscapes illuminate past evolutionary events in the endangered fern Vandenboschia speciosa.
Genome
; 65(2): 95-103, 2022 Feb.
Article
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| MEDLINE
| ID: mdl-34555288
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 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.
Palabras clave
Vandenboschia speciosa; changements démographiques; climate crisis; crise climatique; demographic changes; endangered species; espèce menacées; ferns; fougères; genome size; populations reliques; relict populations; taille du génome; tetraploidy; transposable elements; tétraploïdie; éléments transposables
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1
Bases de datos:
MEDLINE
Asunto principal:
Helechos
Idioma:
En
Revista:
Genome
Asunto de la revista:
GENETICA
Año:
2022
Tipo del documento:
Article
País de afiliación:
España