An Exploration into Fern Genome Space

Abstract

Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (∼0.4X to 2X) for six fern species from the Polypodiales (Ceratopteris, Pteridium, Polypodium, Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of fern genomes can provide information useful for selecting a promising candidate fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between ferns and seed plants.

Keywords: chloroplast; comparative genomics; mitochondria; plastome; repeat content; transposons.

Fig. 1.—

Phylogeny of ferns summarized from Pryer et al. (2004). Numbers of sequenced nuclear genomes are indicated for the lineages that have them. Lineages in pink are the eusporangiate ferns; the leptosporangiate fern clade is in green. Taxa in this study are given in parentheses. Photos of representative ferns are included: (A) Ceratopteris richardii (Pteridaceae); (B) Salvinia sp., Salviniales (heterosporous water ferns); (C) Cystopteris protrusa (Cystopteridaceae); (D) Ophioglossum sp., Ophioglossales (rattlesnake ferns); and (E) Equisetum sp. (horsetails). The timescale along the bottom of the phylogeny is in millions of years before present.

Fig. 2.—

Depth of coverage for primary CLC assemblies plotted as a function of contig length. Axes are log scale and contour lines (blue) show the density of overplotted contigs. Chloroplast contigs are shown in green and mitochondrial contigs are shown in orange.

Fig. 3.—

Genome proportions represented by ten sequence-based repeat classes, plus unknown repeats and nonrepetitive sequences, in six fern and six seed plant taxa, with three samples per taxon.

Fig. 4.—

Scatter plots showing the relationship between proportion of different classes of genomic elements and genome size for ferns and seed plants.