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De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum

Joshua P Der13*, Michael S Barker2, Norman J Wickett3, Claude W dePamphilis3 and Paul G Wolf1

Author Affiliations

1 Department of Biology and Center for Integrated Biosystems, Utah State University, Logan, UT 84322-5305, USA

2 Department of Ecology and Evolutionary Biology, University of Arizona, Tuscon, AZ 85721, USA

3 Department of Biology, Institute of Molecular Evolutionary Genetics, and The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA

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BMC Genomics 2011, 12:99  doi:10.1186/1471-2164-12-99

Published: 8 February 2011

Additional files

Additional file 1:

Unigene builds. Unigene sequences in FASTA format, compressed zip file.

Format: ZIP Size: 9.5MB Download file

Open Data

Additional file 2:

Unigene functional annotations from Blast2GO. GO and EC functional classification for unigenes.

Format: CSV Size: 6.8MB Download file

Open Data

Additional file 3:

Functional annotation enrichment for GO-slim categories relative to the complete Arabidopsis genome. FDR-corrected Fisher exact test for GO-slim categories represented in the Pteridium unigene set and the Arabidopsis genome.

Format: CSV Size: 11KB Download file

Open Data

Additional file 4:

PlantTribes2.0 gene family classification. Tribe and orthogroup assignments for each unigene and cluster membership for the ten proteomes included in PlantTribes2.0. Functional and gene family descriptors for clusters are primarily inherited from the Arabidopsis thaliana genes included in the cluster.

Format: CSV Size: 12.5MB Download file

Open Data

Additional file 5:

SSR loci identified in msatCOMMANDER. Repeat sequence information (repeat motif, location, and lenth) for SSR loci identified by msatCOMMANDER.

Format: CSV Size: 117KB Download file

Open Data

Additional file 6:

Primer sequences and details for SSR loci. Primer sequences for potentially amplifiable SSR loci selected using msatCOMMANDER.

Format: CSV Size: 89KB Download file

Open Data

Additional file 7:

Secondary coverage perl script. Script used to identify singleton reads and primary and secondary contigs and calculate assembly statistics.

Format: PL Size: 16KB Download file

Open Data

Additional file 8:

Unigene accumulation curve perl script. Script to randomly select reads from the assembly and calculate the number of contigs detected to produce the unigene accumulation curve.

Format: PL Size: 4KB Download file

Open Data