Dreaden, Tyler

Our research group studies pathogens of forest trees.  We are interested in clarifying taxonomic relationships among species, identifying causal agents of new diseases, and exploring resistance mechanisms.  The work we do furthers our understanding of the host pathogen systems we study with the ultimate goal of using what we learn to develop disease management strategies that can be deployed in the field.  Two studies are described in more detail below.

Genomics of the Fusiform Rust and Brown Spot Needle Blight Systems

Purpose: Apply novel comparative genomics methods to study the origin of the Lecanosticta acicula outbreak on Loblolly pine and compare historic and contemporary variation in the fusiform rust pathogen (Cronartium quercuum f.sp. fusiforme) with implications for resistance breeding and management.

1) Retrospective study of Lecanosticta acicola: A growing threat to domestic and global pine forests

Objective: Genome wide population genetics study with isolates from: recent needle blight of loblolly pine, longleaf with typical symptoms, historic collections from the southeast (southern lineage) and isolates from the northeast (northern lineage). We will determine if the isolates from the recent outbreak on loblolly pine represent new genotypes, not representative of the historic isolates.  The findings might explain the recent damage on loblolly pine. We will also look for evidence of admixture between the southern and northern lineages, and determine if the lineages should be separate species.

2) Comparing Historic with Contemporary Variation in the Fusiform Rust Pathogen and Implications for Breeding and Management in a Changing Climate

Background: Fusiform rust caused by the fungal pathogen Cronartium quercuum f. sp. fusiforme (Cqf) is endemic on oaks and pines in the southeastern US and can have a devastating impact on the 190 million acers of Southern pine. Estimates for loses by Cqf vary but are likely $100s of millions annually prompting enormously successful research efforts developing host resistance, 4:1 to 6:1 benefit cost ratio. 

Objective: The study will associate the 9 known virulence alleles that overcome specific resistance genes with geographic areas and evaluate the Cqf population over time (the last 35 years), representing a period of enormous change (climactic and wide-spread use of improved families with rust resistance). Results will inform management decisions for deployment of fusiform rust resistance through space/time (ie. deploy resistance genes to match local pathogen population or stacking multiple resistance genes if pathogen virulence alleles vary through time) and determine if the large-scale deployment of resistance coincides with shifts in the pathogen’s population-level virulence or genetic diversity.  We will identify possible Avr genes by doing whole genome sequencing of pycnia spores that develop on galls from susceptible pine families and comparing them to sequences generated from pycnia from galls formed on seven pine families with 9 known Fr genes.

1) Retrospective study of Lecanosticta acicola: A growing threat to domestic and global pine forests

We are collecting isolates from throughout the region, gathering from historic collections and generating genomes for each to do a comparative genomics study with isolate from the current loblolly pine epidemic.  We hope to determine the origin of the isolates causing the current loblolly pine epidemic.

2) Comparing Historic with Contemporary Variation in the Fusiform Rust Pathogen and Implications for Breeding and Management in a Changing Climate

We are inoculating pine families with known fusiform rust resistance genes, control susceptible seedlings, and collect the resulting fungi from the stem galls.  We will generate genomes of the resulting fungi to identify the corresponding Avr genes.  We will then screen a historic collection of fusiform rust to identify the presence of Avr genes across the region and through time.  Results will be used to guide deployment fusiform rust resistant genes.

3) Identify Fungal and Bacterial Endophytes Unique to “Lingering” Ash

We have collected stem samples from “Lingering” ash trees that have persisted after >95% of their piers have sarcoma to emerald ash borer.  We hypothesize that endophyte might be contributing to the phenotype.  We will use amplicon based metagenomics to identify the fungal and bacterial endophytes of “Lingering” and wild type ash to identify genotypes consistently associated with the “Lingering” phenotype.

We will be doing mostly Next Generation genomic sequencing using illumina and nanopore technologies and following mostly standard protocols and software that has already been developed.  Most of the software for base calling, QC, trimming, assembly, and other methods are already installed on the HPC.  We are at the very beginning of these projects and do not have the methodology worked out at this time.  Some software might need to be installed on the HPC, but it would be previously published and should be limited in number.

The methods have not been established yet.  In the beginning we will be processing nanopore reads and using: dorado, canu, flye, guppy, bowtie2, raxml, qiime2, and nucmer.

UK collaborators: Dr. Mark Farman, Dr. Ellen Crocker, Dr. Tetyana Zhebentyayeva

Non UK collaborators: Cady Greenslit, USDA Forest Service