RADseq as a valuable tool for plants with large genomes—A case study in cycads

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...

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Bibliographic Details
Published in:Molecular ecology resources 2019-11, Vol.19 (6), p.1610-1622
Main Authors: Clugston, James A. R., Kenicer, Gregory J., Milne, Richard, Overcast, Isaac, Wilson, Trevor C., Nagalingum, Nathalie S.
Format: Article
Language:English
Subjects:
Assembly
Cycadales
Cycadophyta
cycads
Cycas - genetics
Cyperus calcicola
Datasets
Deoxyribonucleic acid
DNA
DNA sequencing
Genetic Markers - genetics
Genome, Mitochondrial - genetics
Genome, Plant - genetics
Genomes
Genomics - methods
illumina sequencing
large genomes
Loci
Markers
Mitochondria
Natural populations
Organisms
Phylogeny
Plastids
RADseq
Sequence Analysis, DNA - methods
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Summary: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.
ISSN:1755-098X
1755-0998
DOI:10.1111/1755-0998.13085