The C-Fern (Ceratopteris richardii) genome: insights into plant genome evolution with the first partial homosporous fern genome assembly

Ferns are notorious for possessing large genomes and numerous chromosomes. Despite decades of speculation, the processes underlying the expansive genomes of ferns are unclear, largely due to the absence of a sequenced homosporous fern genome. The lack of this crucial resource has not only hindered investigations of evolutionary processes responsible for the unusual genome characteristics of homosporous ferns, but also impeded synthesis of genome evolution across land plants. Here, we used the model fern species Ceratopteris richardii to address the processes (e.g., polyploidy, spread of repeat elements) by which the large genomes and high chromosome numbers typical of homosporous ferns may have evolved and have been maintained. We directly compared repeat compositions in species spanning the green plant tree of life and a diversity of genome sizes, as well as both short- and long-read-based assemblies of Ceratopteris. We found evidence consistent with a single ancient polyploidy event in the evolutionary history of Ceratopteris based on both genomic and cytogenetic data, and on repeat proportions similar to those found in large flowering plant genomes. This study provides a major stepping-stone in the understanding of land plant evolutionary genomics by providing the first homosporous fern reference genome, as well as insights into the processes underlying the formation of these massive genomes.

Nuclear Genome Size is Positively Correlated with Mean LTR Insertion Date in Fern and Lycophyte Genomes

Nuclear genome size is highly variable in vascular plants. The composition of long terminal repeat retrotransposons (LTRs) is a chief mechanism of long term change in the amount of nuclear DNA. Compared to flowering plants, little is known about LTR dynamics in ferns and lycophytes. Drawing upon the availability of recently sequenced fern and lycophyte genomes we investigated these dynamics and placed them in the context of vascular plants. We found that similar to seed plants, mean LTR insertion dates were strongly correlated with haploid nuclear genome size. Fern and lycophyte species with small genomes such as those of the heterosporous Selaginella and members of the Salviniaceae had recent mean LTR insertion dates, whereas species with large genomes such as homosporous ferns had old mean LTR insertion dates intermediate between angiosperms and gymnosperms. This pattern holds despite methylation and life history differences in ferns and lycophytes compared to seed plants, and our results are consistent with other patterns of structural variation in fern and lycophyte genomes.

Effect of Nutrients on Environmental Sex Determination and Size of Gametophytes in Culcita macrocarpa

In environmental sex determination (ESD) gender is decided after conception, depending on the environment, rather than being genetically fixed. ESD has rarely been studied in homosporous ferns. In the present study, Culcita macrocarpa gametophytes were cultured under varying nutrient conditions. Initially, most of the gametophytes of Culcita macrocarpa were male and subsequently hermaphrodite under different nutrition. The result indicates that its sex determination is protandry. All nutrient conditions were favourable for developing male prothalli but only good environment (high nutrient) was favourable for female gametophyte growth. In all respects, female gametophytes were much larger, than the other types of gametophytes. Hermaphroditic gametophytes were larger than male gametophytes, which were larger than asexual gametophytes. DOI: http://dx.doi.org/10.3329/jles.v7i0.20130 J. Life Earth Sci., Vol. 7: 109-113, 2012