Leaf infection by M. americana. Image by Chase Crowell.

M. americana spore pustule. Image by Chase Crowell.

Melampsora willow rust is the most economically devastating disease of shrub willow (Salix), a bioenergy feedstock in much of the world.  Wind dispersed asexual uredospores colonize the leaf tissue of the willow host during the growing season and asexually reproduce at high rates causing polycyclic disease outbreaks.  Heavy infection of susceptible willow genotypes can cause premature leaf senescence resulting in significant yield loss.  Both quantitative and qualitative resistances have been observed in willow, suggesting the existence of promising genetic components within the Salix gene pool useful for the development of resistant willow cultivars.

Melampsora americana (Basidiomycota; Pucciniomycotina;  Pucciniomycetes; Pucciniales; Melampsoraceae) is the causative agent in most cases of Melampsora willow rust on the naturalized willow species Salix purpurea in the northeast United States.  It is a macrocyclic and heteroecious rust alternating on the Abies balsamea (balsam fir), reaching its greatest disease pressure in the late summer to early fall.   Primary signs of infection are small ~0.2 mm diameter discrete orange pustules typically on the abaxial side of willow leaves.  Single celled, sessile teliaspores are believed to be the primary overwintering source, however overwintering uredospores may contribute to the successive year’s disease.  Investigation into the genetic diversity of the pathogen population, with the reference genome as a cornerstone for study, may provide greater insight into the life cycle of this pathogen from year to year. 

Various reduced representation sequencing methods exist for the purpose of population analysis; but many are greatly improved with the addition of a reference genome.  Access to the M. americana genome will enable population diversity studies of M. americana with greater confidence, ensuring accurate read mapping of genotyping-by-sequencing (GBS) tags and genotype calling.  Knowing the diversity of the pathogen population, paired with an understanding of pathogenicity of a range of isolates, will enable more efficient breeding for resistance to willow rust in the northeast United States via the identification and use of genetically diverse isolates as a panel for challenging willow breeding lines. 

Lastly, genomic resources may allow investigation into plant-pathogen interactions. Various other Melampsora spp. rusts have been sequenced and can be used for comparative genomics for genetic insight into the mechanisms of obligate biotrophy and host specificity.  Additionally, a reference genome assembly of the host S. purpurea is publicly available, providing an exciting opportunity for simultaneous host-pathogen genomic investigation.

A virulent Melampsora americana isolate (R15-033-03) collected from a wild S. purpurea shrub in Lafayette, NY in 2015 was submitted through the Community Science Program for whole genome sequencing.  Genomic DNA isolated from uredospores was used to construct 10kb libraries for PacBio sequencing and the resulting genome was assembled using Falcon v. 1.8.8. Additionally, extracted RNA from diseased plant leaf tissue on S. purpurea was collected for improved gene annotation.  RNAseq of total extracted RNAs were mapped against the S. purpurea v1.0 genome and willow transcripts were subtracted for fungal transcript enrichment.