Targeted enrichment sequencing of Phytophthora infestans and Solanum hosts
Two bait libraries were designed based on the genes of interest (Daicel Arbor Biosciences). For the pathogen, Phytophthora infestans, a list of known RXLR genes was compiled from the T30-4 reference genome as well as a handful of other published RXLR genes [44]. From this list of 568 known RXLR reference genes, 8,105 bait sequences, each approximately 80 nucleotides in length, were designed for RXLR target capture. For the host, Solanum spp., a list of 117 R genes for late blight resistance (and one for daylength tolerance, StCDF1) was compiled from the SolTub3.0 genome and other published resources involving potato wild relatives. Using these 117 input R genes, 8,647 baits, each 80 nucleotides in length, were generated. Both sets of baits were designed to match the target input genes (listed RXLRs and R genes) as well as any highly similar loci. The bait design focused on the regions of interest, excluding repeat-rich regions. Additionally, a Blast search was conducted against the relevant genomes to ensure that there were not a high number of off-target alignment sites.Samples were sequenced on a NovaSeq with 150bp paired-end reads by Arbor Biosciences myReads (Ann Arbor, MI).