Comparative Exploration of Fern Genome Space

Ferns represent 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, including their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a low coverage (0.25-2X) whole genome shotgun approach to obtain sequence information for six leptosporangiate ferns sampled across the phylogeny: Dipteris conjugata (Gleicheniales), Plagiogyria formosana (Cyatheales), Pteridium aquilinum (Dennstaedtiaceae), Ceratopteris richardii (Pteridaceae), Polypodium glycyrrhiza (eupolypods I), and Cystopteris protrusa (eupolypods II). We explore these data to characterize the proportion of the nuclear genome represented by protein-coding genes and repetitive sequences (including transposons, rDNA, and satellite elements), as well as to extract chloroplast and mitochondrial genome sequences. This initial examination of fern genome space enables us to characterize variation for genomic traits across ferns and make a preliminary comparison with seed plant genomes. The model fern, Ceratopteris richardii, has been targeted for additional deep sequencing  by the pteridological community to develop a draft reference sequence for a homosporous fern.