Development and evaluation of a target enrichment bait set for next generation sequencing of the potato wart pathogen, Synchytrium endobioticum

Potato wart disease is caused by an obligate fungal pathogen Synchytrium endobioticum. While working with this fungus, samples from compost, purified spores and crude wart tissue derived from tuber galls of infected potatoes can sometimes have low S. endobioticum DNA concentration or are highly contaminated with other microorganisms or material from the potato host. Because of this, Illumina sequencing using DNA extracted from this material often results in suboptimal recovery of the nuclear genome sequences of this pathogen. A hybridization-based target enrichment protocol was developed to enhance the recovery of S. endobioticum DNA, leaving DNA from off target organisms behind.