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Description
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.
Publisher
Botanical Society of America
Publication Date
7-28-2014
Keywords
genomics, ferns, organelle genomes, mitochondrial genome, plastid genome
Disciplines
Genetics and Genomics | Plant Sciences
Recommended Citation
Wolf, Paul G.; Sessa, Emily B.; Marchant, D. Blaine; Li, Fay-Wei; Rothfels, Carl J.; Sigel, Erin M.; Gitzendanner, Mathew A.; Visger, Clayton J.; Banks, Jo Ann; Soltis, Douglas E.; Soltis, Pamela S.; Pryer, Kathleen M.; and Der, Joshua P., "An Exploration of Fern Genome Space" (2014). An Exploration of Fern Genome Space. 1.
https://digitalcommons.usu.edu/fern_genome/1