Trials and Tribulations of Using RADseq for Large and Complex Genomes

Dr. Sally M Chambers, Marie Selby Botanical Gardens

Next generation sequencing technologies have rapidly developed over the past decade, providing new avenues for scientists working on non-model organisms to study patterns at the genome level. Techniques can be used to drastically simplify a complex genome and multiplex samples, which help make these sequencing platforms more cost effective than traditional methods when standardized by the amount of data generated. However, a number of factors need to be taken into account when developing a next-generation sequencing project, including genome size and complexity. Ferns are well known for having large and complex genomes, as many lineages are characterized by reticulate evolution. This produces species complexes that contain multiple hybrid individuals. Based on recent experiences in developing a study to resolve relationships within a species complex of North American Dryopteris, the applicability of double-digest RAD sequencing proved difficult. Lessons learned from this experience will be shared in order to assist others that would like to apply RADseq technologies to taxa with large or complex genomes.