Characterization of the satellitome in lower vascular plants: the case of the endangered fern Vandenboschia speciosa

• Published in: Annals of botany Vol. 123; no. 4; pp. 587 - 599
• Main Authors: Ruiz-Ruano, F J, Navarro-Domínguez, B, Camacho, J P M, Garrido-Ramos, M A
• Format: Journal Article
• Language: English
• Published: US Oxford University Press 14-03-2019
• Subjects: Base Sequence; Diploidy; DNA, Plant - analysis; DNA, Satellite - analysis; Evolution, Molecular; Ferns - genetics; Genome, Plant; Germ Cells, Plant - physiology; Haploidy; Original; Reproduction; ferns; reproduction mode; satDNA; satellite DNA evolution; phase alternation; gametophyte; transposable elements; satellitome; sporophyte; Vandenboschia speciosa
• ISSN: 0305-7364; 1095-8290
• DOI: 10.1093/aob/mcy192

Abstract
Background and Aims
Vandenboschia speciosa is a highly vulnerable fern species, with a large genome (10.5 Gb). Haploid gametophytes and diploid sporophytes are perennial, can reproduce vegetatively, and certain populations are composed only of independent gametophytes. These features make this fern a good model: (1) for high-throughput analysis of satellite DNA (satDNA) to investigate possible evolutionary trends in satDNA sequence features; (2) to determine the relative contribution of satDNA and other repetitive DNAs to its large genome; and (3) to analyse whether the reproduction mode or phase alternation between long-lasting haploid and diploid stages influences satDNA abundance or divergence.
Methods
We analysed the repetitive fraction of the genome of this species in three different populations (one comprised only of independent gametophytes) using Illumina sequencing and bioinformatic analysis with RepeatExplorer and satMiner.
Key Results
The satellitome of V. speciosa is composed of 11 satDNA families, most of them showing a short repeat length and being A + T rich. Some satDNAs had complex repeats composed of sub-repeats, showing high similarity to shorter satDNAs. Three families had particular structural features and highly conserved motifs. SatDNA only amounts to approx. 0.4 % of its genome. Likewise, microsatellites do not represent more than 2 %, but transposable elements (TEs) represent approx. 50 % of the sporophytic genomes. We found high resemblance in satDNA abundance and divergence between both gametophyte and sporophyte samples from the same population and between populations.
Conclusions
(1) Longer (and older) satellites in V. speciosa have a higher A + T content and evolve from shorter ones and, in some cases, microsatellites were a source of new satDNAs; (2) the satellitome does not explain the huge genome size in this species while TEs are the major repetitive component of the V. speciosa genome and mostly contribute to its large genome; and (3) reproduction mode or phase alternation between gametophytes and sporophytes does not entail accumulation or divergence of satellites.