The Combination of Target Enrichment and Genome Skimming (Hyb-Seq) for Phylogenetic Reconstruction of South African Oxalis (Oxalidaceae)

The introduction of high-throughput sequencing (HTS) technologies to plant systematics has the potential to greatly increase the amount of phylogenetically informative signal. Difficulties in phylogenetic reconstructions such as polytomies and low support values are expected to be at least partly overcome, as they are often the result of using only a small fraction of the genome. When HTS was introduced to plant phylogenetics, sequencing of the plastid genome was its first focus. Later approaches of genome skimming, the sequencing of the high-copy fractions of the nuclear, plastid and mitochondrial genome, resulted in the assembly of the nrDNA cistron and nearly the complete plastid and mitochondrial genome. Currently, target enrichment of low-copy, orthologous nuclear exons is becoming increasingly popular, but up to now these loci have only rarely been used for plant phylogenetics (e.g., genus Asclepias (Apocynaceae), Asteraceae, genus Oxalis (Oxalidaceae) - this poster). In the case of Oxalis target enrichment of low-copy nuclear genes was combined with genome skimming (Hyb-Seq). Target enrichment probes were designed based on a combination of transcriptome and genome skim data and tested on 24 South African Oxalis species, resulting in a well-supported phylogeny with all nodes resolved. This case study demonstrates that Hyb-Seq has a very promising future in phylogenomics, especially if one considers that there will be increasing accessibility to reference transcriptomes/genomes, increasing capacity of HTS platforms and steadily improving multiplex options.