Phylotranscriptomics of Ferns and Lycophytes, Two Key Lineages in Land-Plant Evolution

Despite their central position in land-plant phylogeny, there are very few genomic resources available for ferns or lycophytes, aside from a genome produced in 2011 for the lycophyte Selaginella. Ferns and lycophytes are key plant groups, as they represent, respectively, the sister group of seed plants (including flowering plants), and the sister group of all remaining vascular plants. These plants are therefore important for understanding the molecular evolution of the genomes of model plants like Arabidopsis, and the evolution of key plant traits including vascular tissue and heterospory. Here we describe new phylotranscriptomic resources produced for 100 ferns and lycophytes by the 1KP Consortium, a subset of over one thousand Illumina-based transcriptomes produced for the green-plant tree of life. These transcriptomes represent all of the major fern and lycophyte lineages, and comprise 78 fern (monilophyte) species, including the major eusporangiate and leptosporangiate lineages, and 22 lycophytes (representing all three families). Using these novel data, we revisit classical and contemporary phylogenetic hypotheses for higher-order relationships in ferns and lycophytes, which to date have been based on only a handful of loci. We also discuss these new phylotranscriptomic resources in the context of other proposed and ongoing genomic and transcriptomic studies for ferns.