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Home > Data Services > Datasets > Fern Genome

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An Exploration of Fern Genome Space

 
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  • CLC Assemblies by 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

    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.

  • Compressed Cleaned Reads by 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

    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.

  • Fern Mitochondrial Gene Analysis by 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 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).

  • Raw Reads by 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

    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.

  • An Exploration of Fern Genome Space by 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

    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.

 
 
 

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