An Exploration of Fern Genome Space

Paul G. Wolf, Utah State University
Joshua Der, Pennsylvania State University - Main Campus
Fay-Wei Li, Duke University
Carl J. Rothfels, University of British Columbia
Mathew A. Gitzendanner, University of Florida
Clayton J. Visger, University of Florida
Marchant D. Blaine, University of Florida
Douglas E. Soltis, University of Florida
Pamela S. Soltis, University of Florida
Kathleen M. Pryer, Duke University

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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 (1X 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 protein-coding genes and repetitive sequences (including transposons, rDNA, and satellite elements), as well as 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.