An Exploration of Fern Genome Space

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  CLC Assemblies

  Paul G. Wolf, Joshua P. Der, Fay-Wei Li, Carl J. Rothfels, Mathew A. Gitzendanner, Clayton J. Visger, D. Blaine Marchant, Douglas E. Soltis, Pamela S. Soltis, Kathleen M. Pryer, Emily B. Sessa, Erin M. Sigel, and Jo Ann Banks

  Fern genome sequence data for six species, assembled using CLC Assembly Cell (v4.2.1). Details of assemblies provided in seq_stats.txt.

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  Compressed Cleaned Reads

  Paul G. Wolf, Joshua P. Der, Fay-Wei Li, Carl J. Rothfels, Mathew A. Gitzendanner, Clayton J. Visger, D. Blaine Marchant, Douglas E. Soltis, Pamela S. Soltis, Kathleen M. Pryer, Emily B. Sessa, Erin M. Sigel, and Jo Ann Banks

  Genome sequence data for six fern species, Illumina reads (in fastq format) with adapters removed using catadapt and quality trimmed using sickle. Files compressed using bzip2.

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  Fern Mitochondrial Gene Analysis

  Paul G. Wolf, Joshua P. Der, Fay-Wei Li, Carl J. Rothfels, Mathew A. Gitzendanner, Clayton J. Visger, D. Blaine Marchant, Douglas E. Soltis, Pamela S. Soltis, Kathleen M. Pryer, Emily B. Sessa, Erin M. Sigel, and Jo Ann Banks

  Contigs containing putative mitochondrial genes for each of six fern species. Details for building the initial list of core mitochondrial genes provided in core_mito_gene_notebook.zip (an ipython notebook).

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  Raw Reads

  Paul G. Wolf, Joshua P. Der, Fay-Wei Li, Carl J. Rothfels, Mathew A. Gitzendanner, Clayton J. Visger, D. Blaine Marchant, Douglas E. Soltis, Pamela S. Soltis, Kathleen M. Pryer, Emily B. Sessa, Erin M. Sigel, and Jo Ann Banks

  Original (unprocessed) paired-end Illumina Reads for genomic data from six fern species, compressed using gzip.

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  An Exploration of Fern Genome Space

  Paul G. Wolf, Emily B. Sessa, D. Blaine Marchant, Fay-Wei Li, Carl J. Rothfels, Erin M. Sigel, Mathew A. Gitzendanner, Clayton J. Visger, Jo Ann Banks, Douglas E. Soltis, Pamela S. Soltis, Kathleen M. Pryer, and Joshua P. Der

  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.