Format: ORAL

Christoph Nehrke, Mareike Daubert, Eike Mayland-Quellhorst Dirk C. Albach

Carl-von-Ossietzky University Oldenburg, 26129 Oldenburg, Germany

Recent improvements in genome sequencing, especially long read sequencing techniques like Oxford Nanopore sequencing, provide the means to assemble high quality (draft) genomes for a plethora of species. While these genomes find uses in multiple fields of life sciences, a common application for them is to serve as references in the assembly of high-throughput sequencing reads in phylogenomics. However, it is unclear how quality and phylogenetic position of a reference relative to the investigated dataset influence phylogenomic assemblies and topology of phylogenetic trees. To answer this question, we sequenced and assembled genomes of seven species of Veronica, a plant genus known for polyploidization, frequent hybridization and high speciation rates, using Oxford Nanopore sequencing in combination with high coverage Illumina sequencing reads. The assembled references were tested for quality, completeness, contiguity, and possible contaminants. A Genotyping-by-sequencing dataset including 72 samples from Veronica subg. Pseudolysimachium was assembled denovo, as well as reference-assisted with different parameters, using each draft genome as a reference. We found that not only alignment lengths and number of retrieved loci are changing among the different reference genomes, but also tree topologies and branch lengths, depending on reference taxon and reference quality. These variable results may lead to false conclusions regarding the evolutionary history of the subgenus.