Sessa, E. B., & Der, J. P. (2016). Evolutionary Genomics of Ferns and Lycophytes. In S. A. Rensing (Ed.), Genomes and Evolution of Charophytes, Bryophytes, Lycophytes and Ferns (pp. 215–254).
Abstract: Ferns and lycophytes are ubiquitous and charismatic members of many terrestrial ecosystems. Members of these lineages play key ecological roles in many of Earth’s biomes and have an ancient fossil record dating back to the Devonian. Modern ferns underwent significant diversification in the Cretaceous, and the clade as a whole occupies a pivotal position in land plant evolution as the sister lineage to seed plants; lycophytes, in turn, are sister to ferns plus seed plants together. Both ferns and lycophytes are spore-bearing vascular plants, and each clade includes both homospo- rous and heterosporous members. Many taxa have large genomes with high numbers of chromosomes, particularly among the homosporous members of both lineages. They are the only two lineages of land plants that maintain independent gametophyte and sporophyte phases in their life cycle. Ferns are known to be prone to hybridization and polyploidy, but the roles these events have played in producing their large genomes are still unclear. Genome science has advanced dramatically in recent years, but genomic research in lycophytes and ferns has lagged behind other groups of plants. While nuclear genome sequences are now available for over 100 species of seed plants, there is only one sequenced genome of a lycophyte available (heterospo- rous Selaginella moellendorffii), and none from any fern, or from any homosporous vascular plant. This chapter reviews what is known about fern and lycophyte genomes (nuclear, chloroplast, and mitochondrial) and transcriptomes and presents an outlook on the future of genome research in these groups, including outstanding challenges in plant biology that will be illuminated by incorporating information on ferns and lycophytes.