Full genome sequencing of organisms with large and complex genomes is intractable and cost ineffective under most research budgets. Cycads (Cycadales) represent one of the oldest lineages of the extant seed plants and, partly due to their age, have incredibly large genomes up to ~60 Gbp. Restriction site‐associated DNA sequencing (RADseq) offers an approach to find genome‐wide informative markers and has proven to be effective with both model and nonmodel organisms. We tested the application of RADseq using ezRAD across all 10 genera of the Cycadales including an example data set of Cycas calcicola representing 72 samples from natural populations. Using previously available plastid and mitochondrial genomes as references, reads were mapped recovering plastid and mitochondrial genome regions and nuclear markers for all of the genera. De novo assembly generated up to 138,407 high‐depth clusters and up to 1,705 phylogenetically informative loci for the genera, and 4,421 loci for the example assembly of C. calcicola. The number of loci recovered by de novo assembly was lower than previous RADseq studies, yet still sufficient for downstream analysis. However, the number of markers could be increased by relaxing our assembly parameters, especially for the C. calcicola data set. Our results demonstrate the successful application of RADseq across the Cycadales to generate a large number of markers for all genomic compartments, despite the large number of plastids present in a typical plant cell. Our modified protocol was adapted to be applied to cycads and other organisms with large genomes to yield many informative genome‐wide markers.
The Cycadales are a group of significant global conservation concern and have the highest extinction risk of all seed plants. Understanding the synchronisation of reproductive phenology of Cycadales may be useful for conservation by enabling the targeting of pollen and seed collection from wild populations and identifying the window of fertilisation to aid in the cultivation of Cycadales. Phenological data for 11 species of Zamia were gathered from herbarium specimens. Four phenological characters were coded with monthly character states. DNA was isolated and sequenced for 26S, CAB, NEEDLY, matK and rbcL, and a simultaneous phylogenetic analysis of phenology and DNA sequence data was carried out. Three major clades were recovered: a Caribbean clade, a Central American clade and a South American clade. Eight species showed statistically significant synchronisation in microsporangiate and ovulate phenological phases, indicating the time of fertilisation. Close reproductive synchronisation was consistently observed throughout the Caribbean clade (statistically significant in four of five species) but was less consistent in the Central American clade (statistically significant in one of two species) and South American clade (statistically significant in three of four species). Ultimately, phenology is shown to be a potential driver of speciation in some clades of Zamia and in others to be a potential barrier to hybridisation.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.