Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain.
Ann Bot. 2019 Mar 14;123(4):587-599. doi: 10.1093/aob/mcy192.
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.
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.
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.
(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.
Vandenboschia speciosa 是一种高度脆弱的蕨类植物，其基因组较大（10.5Gb）。单倍体配子体和二倍体孢子体为多年生植物，可进行营养繁殖，某些种群仅由独立的配子体组成。这些特征使得这种蕨类植物成为一个很好的模型：（1）用于高通量分析卫星 DNA（satDNA），以研究 satDNA 序列特征的可能进化趋势；（2）确定 satDNA 和其他重复 DNA 对其大基因组的相对贡献；（3）分析持久的单倍体和二倍体阶段之间的繁殖模式或交替是否影响 satDNA 的丰度或分化。
我们使用 Illumina 测序和 RepeatExplorer 和 satMiner 等生物信息学分析，对该物种的三个不同种群（一个种群仅由独立的配子体组成）的基因组重复部分进行了分析。
V. speciosa 的卫星组由 11 个 satDNA 家族组成，其中大多数具有短重复长度且富含 A+T。一些 satDNA 具有由亚重复组成的复杂重复，与较短的 satDNA 高度相似。三个家族具有特殊的结构特征和高度保守的基序。satDNA 仅占其基因组的约 0.4%。同样，微卫星也不超过 2%，但转座元件（TEs）占孢子体基因组的约 50%。我们发现，来自同一种群的配子体和孢子体样本以及不同种群之间的 satDNA 丰度和分化具有高度相似性。
（1）V. speciosa 中较长（且较老）的卫星具有较高的 A+T 含量，并且是从较短的卫星进化而来的，在某些情况下，微卫星是新 satDNA 的来源；（2）卫星组并不能解释该物种巨大的基因组大小，而 TEs 是 V. speciosa 基因组的主要重复成分，主要贡献了其基因组的大小；（3）配子体和孢子体之间的繁殖模式或交替不会导致卫星的积累或分化。
