PRJNA668013
RADseq data of Pacific Northwest Cenococcum geophilum isolate collection
Restriction-associated DNA sequencing (RADseq) methods have been used in various animal and plant species for SNP detection and increased species-level resolution of phylogenetic patterns and understanding population level gene flow (DaCosta and Sorenson, 2016; Davik et al., 2015; Grewe et al., 2018, 2017; Kai et al., 2014; Kess et al., 2015; Shirasawa et al., 2017; Toonen et al., 2013), but rarely applied to fungi (Grewe et al., 2018, 2017). This method has been proposed as a potential alternative to whole-genome sequencing (Andrews et al., 2016; Obase et al., 2017) at a fraction of the cost (Bayona-Vasquez et al., 2019; Graham et al., 2015; Hoffberg et al., 2016; Toonen et al., 2013) while providing a snapshot of genetic variation across the genome. The RADseq method also does not require prior genomic information in order to complete downstream analyses (Andrews et al., 2016), making this a powerful tool which can be used in either de novo or reference-based sequencing data assemblies. In order to test the viability of this process with a collection of C. geophilum isolates, the 3RAD RADseq method (Bayona-Vasquez et al., 2019) was applied to a total of 187 of the Velez et al. (2020) PNW strains in order alleviate previous limitations from low phylogenetic resolution within the collection based on gene-based approaches. Because this method has rarely been applied to fungi, we evaluated various approaches using both reference-based and de novo methods to determine the best bioinformatic approach for analyzing these sequencing data (Shafer et al., 2017). We additionally compare our results to the most common single gene marker (GPD) to directly assess the improvements in the phylogenetic signal based this new approach.