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

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.

Ruiz-Ruano et al. 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.

They found that 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. Interestingly, 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. They also found that reproduction mode or phase alternation between gametophytes and sporophytes does not entail accumulation or divergence of satellites.