De novogenome assembly ofGeosmithia morbida, the causal agent of thousand cankers disease

Abstract

Geosmithia morbida is a filamentous ascomycete that causes thousand cankers disease in the eastern black walnut tree. This pathogen is commonly found in the western U.S.; however, recently the disease was also detected in several eastern states where the black walnut lumber industry is concentrated. G. morbida is one of two known phytopathogens within the genus Geosmithia, and it is vectored into the host tree via the walnut twig beetle. We present the first de novo draft genome of G. morbida. It is 26.5 Mbp in length and contains less than 1% repetitive elements. The genome possesses an estimated 6,273 genes, 277 of which are predicted to encode proteins with unknown functions. Approximately 31.5% of the proteins in G. morbida are homologous to proteins involved in pathogenicity, and 5.6% of the proteins contain signal peptides that indicate these proteins are secreted. Several studies have investigated the evolution of pathogenicity in pathogens of agricultural crops; forest fungal pathogens are often neglected because research efforts are focused on food crops. G. morbida is one of the few tree phytopathogens to be sequenced, assembled and annotated. The first draft genome of G. morbida serves as a valuable tool for comprehending the underlying molecular and evolutionary mechanisms behind pathogenesis within the Geosmithia genus.

Thousand Cankers Disease Complex: A Forest Health Issue that Threatens Juglans Species across the U.S.

“…The G. morbida genome (26.5 Mbp) has recently been sequenced, revealing less than 1% repetition within its more than 6000 genes [35]. A genome-enabled research approach focused on G. morbida can provide a better understanding of the biology of the pathogen involved in TCD and identify candidate genes and functions required for pathogenesis.…”

“…Without an insight into the pathogenicity and mechanisms by which G. morbida overcomes walnut defenses, our ability to predict, prevent, and manage TCD epidemics will be extremely limited. Thus, additional genomic research based on Schuelke et al will serve as a valuable tool for further investigation into the pathogenesis of G. morbida and related forest diseases [35].…”

Apollo: Democratizing genome annotation

“…To date, the i5K Workspace has supported publication of seven insect genomes that were manually curated with Apollo (11)(12)(13)(14)(15)(16)(17). Other projects that have used Apollo include genomes of additional insects (18)(19)(20), human parasites (21)(22)(23), birds (24,25), the sea lamprey (26), plants (27)(28)(29), fungi (30)(31)(32)(33)(34)(35) and a plant pathogenic nematode (36). Projects such as the re-annotation of the whipworm genome by hundreds of high school students in the UK, supported by the Institute for Research in Schools (IRIS) (37), and the curation of 33,044 gene loci in the kiwifruit genome by 93 annotators, are evidence of Apollo's robust support for large dispersed projects.…”

Comparative genomics of beetle-vectored fungal pathogens reveals a reduction in genome size and independent evolution of pathogenicity of two tree pathogens

“…We recently developed a reference genome of Geosmithia morbida that consisted of 73 scaffolds totaling 26.5 Mbp in length (Schuelke et al , 2016). This genome represents one of the smaller fungal tree pathogen genomes reported to date.…”

“…Genome expansions were associated with parasitism in general and increased pathogenicity and virulence in several fungal lineages (Spanu et al , 2010). Previous genome sequencing of Geosmithia morbida (Schuelke et al , 2016) showed that this newly emerged fungal pathogen has a smaller genome than several of its closely related nonpathogenic relatives in the Hypocreales. Hence, Geosmithia has taken an evolutionary path to pathogenicity that has not been characterized previously in plant-associated fungi.…”