A paper reporting the results of genome skimming studies on six ferns, led by Paul Wolf, has been accepted for publication by Genome Biology and Evolution. This is the first study of whole genome content in ferns, and in particular the first data on repeat structure in fern genomes.
Wolf PG, EB Sessa, DB Marchant, F-W Li, CJ Rothfels, EM Sigel, MA Gitzendanner, CJ Visger, JA Banks, DE Soltis, PS Soltis, KM Pryer, JP Der. (2015) An exploration into fern genome space. Genome Biology and Evolution 7(9):2533–2544. PDF
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, rDNA, 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: comparative genomics, plastome, chloroplast, mitochondrial, repeat content, transposons.