Transcriptome of an Armillaria root disease pathogen reveals candidate genes involved in host substrate utilization at the host–pathogen interface

Abstract

Summary Armillaria species display diverse ecological roles ranging from beneficial saprobe to virulent pathogen. Armillaria solidipes (formerly A. ostoyae), a causal agent of Armillaria root disease, is a virulent primary pathogen with a broad host range of woody plants across the Northern Hemisphere. This white‐rot pathogen grows between trees as rhizomorphs and attacks sapwood as mycelial fans under the bark. Armillaria root disease is responsible for reduced forest productivity due to direct tree mortality and non‐lethal infections that impact growth. Here, we characterize a transcriptome of a widespread, virulent genet (vegetative clone) of A. solidipes isolated from a mycelial fan on a natural grand fir (Abies grandis) sapling in northern Idaho, USA. cDNA from polyA+‐purified total RNA was sequenced using a single‐end read approach on the Illumina GAIIx platform which generated 24 170 384 reads. A BLASTx search against the NCBI nr database using 39 943 de novo assembled contigs resulted in 24 442 sequences with significant hits (e‐value < 1e−3), predominantly to fungi (85%). A filtered data set of 20 882 assembled transcripts that encoded putative homologous fungal proteins was created and used for all subsequent analyses. Signal P identified 10 668 putative signal peptides from these fungal transcripts, and 14 360 were annotated with gene ontology terms. Several sequences showed strong homology to annotated genes with functions in pathogenesis, specifically those involved in plant cell wall degradation and response to the post‐infection host environment. This transcriptome contributes to the growing body of resources for studies on fungal pathogens of woody plants, and our results provide useful insights towards identifying specific genes with potential roles associated with pathogenesis and other metabolic functions.

Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

“…Despite their huge impact on forestry, horticulture and agriculture, the genetics of the pathogenicity of Armillaria species is poorly understood. The only -omics data published so far have highlighted a substantial repertoire of plant cell wall degrading enzymes (PCWDE) and secreted proteins, among others, in A. mellea and A. solidipes 11,12 , while analyses of the genomes of other pathogenic basidiomycetes (such as Moniliophthora 13,14 , Heterobasidion 15 and Rhizoctonia 16 ) identified genes coding for PCWDEs, secreted and effector proteins or secondary metabolism (SM) as putative pathogenicity factors. However, the lifecycle and unique dispersal strategy of Armillaria prefigure other evolutionary routes to pathogenicity, which, along with other potential genomic factors (such as transposable elements 17 ) are not yet known.…”

The good, the bad and the tasty: The many roles of mushrooms

“…Basidiospores are unimportant in infection and no asexual reproductive stage is known (Mwenje et al., 1998, Rizzo et al., 1998, Hood et al., 2008). To penetrate plant roots, rhizomorphs grow appressed to the root surface and produce lateral branches that secrete an assortment of cell wall degrading enzymes such as laccases, pectin lyases, peroxidases, polygalacturonases and suberinases (Mwenje and Ride, 1999, Baumgartner et al., 2011, Ross-Davis et al., 2013). After penetrating the root, hyphae subsequently spread through the phloem and secondary xylem in parallel to the cambium and colonise the surrounding tissues, growing as a mycelial fan through the roots and causing necrotic lesions (Fig.…”

“…2013) which has revealed a 58.35 Mb genome, proteomic and transcriptomic data (Collins et al., 2013, Ross-Davis et al., 2013), an Agrobacterium tumefaciens -based method for transformation of basidiospores (Baumgartner et al. 2010) together with a system of producing basidiospores in vitro (Ford et al.…”

Gene expression profiling of candidate virulence factors in the laminated root rot pathogen Phellinus sulphurascens

“…[7, 8, 19]. Less is known about the fungal component of these pathosystems, although recent studies have begun to shed light on molecular strategies utilized by the pathogens [12–19]. The current study represents the first analysis of genes expressed by the causal agent of laminated root rot, Phellinus sulphurascens .…”

“…A small but growing number of studies have examined genes expressed in conifer pathogens, including Armillaria solidipes , a white-rot root disease pathogen [12], Grosmannia clavigera , a mountain pine beetle-associated pathogen of lodgepole pine [13, 14], and Heterobasidion annosum sensu lato , a complex of closely related white-rot basidiomycetes that causes wood-decay in pine, spruce and fir trees [15–17], reviewed in [18]. In this study, we utilized expressed sequence tag (EST) sequencing to discover some of the fungal genes expressed during the Ps -DF interaction.…”