Capturing single‐copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae

With the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming been widely used to obtain high-copy fractions genomes, including plastomes, mitochondrial DNA (mtDNA), nuclear ribosomal (nrDNA). In this study, through simulations, we evaluated optimal (minimum) depth performance for recovering single-copy genes (SCNs) from genome data, by subsampling resequencing data generating 10 sets with different coverage silico. We tested four (plastome, nrDNA, mtDNA, SCNs) obtained based on phylogenetic analyses Vitis clade at genus level Vitaceae family level, respectively. Our results showed that minimum high-quality SCNs assembly via was about 10× coverage. Without steps synthesizing baits enrichment experiments, coupled incredibly low costs, showcase deep (DGS) is as effective capturing large Hyb-Seq approach, addition entire nrDNA repeats. DGS may serve an efficient economical alternative be superior popular target enrichment/Hyb-Seq approach.