CHARACTERIZING THE GENETIC BASIS OF EMERGENCE OF THE HEMLOCK PATHOGEN PHYTOPHTHORA PLUVIALIS

Main Objective: We will develop crucial resources to investigate the genomic basis of adaptation and host shift from Douglas-fir to other hosts such as western hemlock. The specific aims are:Aim 1. Generate a high-quality reference genome for P. pluvialis from a strain collected from Douglas-fir. Rationale. This reference genome will provide a critical resource for aims 2 and 3.I. Long-read sequencingII. Genome assembly and annotationAim 2. Test if populations collected from Douglas-fir and western hemlock plantations are genetically differentiated from each other and from populations collected from wildland forests. Rationale. To assess whether genetic differences may contribute to adaptation to western hemlock, we must first examine whether populations are differentiated by host of origin.H1. Populations of P. pluvialis from western hemlock, Douglas- fir, and native wildland forests are genetically differentiated1. Sample collectionII. Isolations, library preparation, sequencing, and variant callingIII. Population differentiationAim 3. Test if populations that are genetically differentiated and form distinct genetic clusters are also differentiated by host phenotype (disease severity by host).Rationale. To lay the groundwork for understanding the adaptation of P. pluvialis to novel hosts, it is necessary to test whether pathogen populations differ in pathogenicity on each host. This will enable a more pointed comparative genomics analysis.H2. Populations of P. pluvialis from western hemlock, Douglas-fir, and wildland forests differ in pathogenicity on each host.I. Inoculation experimentsII. Comparative genomics analysis