An Exploration into Fern Genome Space

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

Compressed Cleaned Reads

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.https://digitalcommons.usu.edu/fern_genome/1002/thumbnail.jp

An Exploration of Fern Genome Space

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.https://digitalcommons.usu.edu/fern_genome/1000/thumbnail.jp

CLC Assemblies

Fern genome sequence data for six species, assembled using CLC Assembly Cell (v4.2.1). Details of assemblies provided in seq_stats.txt.https://digitalcommons.usu.edu/fern_genome/1001/thumbnail.jp

Fern Mitochondrial Gene Analysis

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).https://digitalcommons.usu.edu/fern_genome/1005/thumbnail.jp

Raw Reads

Original (unprocessed) paired-end Illumina Reads for genomic data from six fern species, compressed using gzip.https://digitalcommons.usu.edu/fern_genome/1004/thumbnail.jp