Fern Genomic Resources

Ferns have historically lagged behind angiosperms in the availability of genomic resources, but such resources are starting to be developed.


Fern Nuclear Genomes

The full, annotated, nuclear genome sequences of the waterferns Azolla and Salvinia have been published, as has that of the model homosporous fern Ceratopteris richardii and that of the tree fern Alsophila spinulosa. Fern are in the genomic age!

In addition, we have some low-coverage genome skimming data available, from the study of Wolf et al. 2015.


Fern Transcriptomes

Much of the increase in fern genomic data available has been in the form of transcriptomes, many of which have been generated by the 1000 Plants Project (1KP). BLAST access to the 1KP transcriptomes is available here, and additional data are available upon request.


Fern Plastomes

A list of available fern plastome sequences (sequences of the chloroplast genome) is available here.


Alignments of low-copy nuclear markers

As part of our study mining transcriptome data for low-copy nuclear markers that could be used in fern phylogenetics (and designing primers for them), we generated lovingly hand-curated alignments of nine gene families. These alignments were available on TreeBASE, but that site is no longer being maintained, so I’ll repost them here. My hope is that these alignments will facilitate additional development of nuclear markers for ferns, particularly (given my biases) for amplicon-based “polyploid phylogenetics”, potentially utilizing (cough-cough) something like PURC (see pub here). Each alignment contains a broad taxon sample, spanning fern diversity (and often including seed plant representatives for context). Generally speaking, only the most conserved domains are confidently alignable; the other portions of the sequences are present but marked as “excluded”.

Alignments: ApPEFP; CRY (focusing on CRY2 and CRY4); det1; GAP (focusing on gapCp “short”); IBR3; pgiC; SQD1; TPLATE; transducin.