Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases

Abstract

BackgroundThe basidiomycete Moniliophthora roreri is the causal agent of Frosty pod rot (FPR) disease of cacao (Theobroma cacao), the source of chocolate, and FPR is one of the most destructive diseases of this important perennial crop in the Americas. This hemibiotroph infects only cacao pods and has an extended biotrophic phase lasting up to sixty days, culminating in plant necrosis and sporulation of the fungus without the formation of a basidiocarp.ResultsWe sequenced and assembled 52.3 Mb into 3,298 contigs that represent the M. roreri genome. Of the 17,920 predicted open reading frames (OFRs), 13,760 were validated by RNA-Seq. Using read count data from RNA sequencing of cacao pods at 30 and 60 days post infection, differential gene expression was estimated for the biotrophic and necrotrophic phases of this plant-pathogen interaction. The sequencing data were used to develop a genome based secretome for the infected pods. Of the 1,535 genes encoding putative secreted proteins, 1,355 were expressed in the biotrophic and necrotrophic phases. Analysis of the data revealed secretome gene expression that correlated with infection and intercellular growth in the biotrophic phase and invasive growth and plant cellular death in the necrotrophic phase.ConclusionsGenome sequencing and RNA-Seq was used to determine and validate the Moniliophthora roreri genome and secretome. High sequence identity between Moniliophthora roreri genes and Moniliophthora perniciosa genes supports the taxonomic relationship with Moniliophthora perniciosa and the relatedness of this fungus to other basidiomycetes. Analysis of RNA-Seq data from infected plant tissues revealed differentially expressed genes in the biotrophic and necrotrophic phases. The secreted protein genes that were upregulated in the biotrophic phase are primarily associated with breakdown of the intercellular matrix and modification of the fungal mycelia, possibly to mask the fungus from plant defenses. Based on the transcriptome data, the upregulated secreted proteins in the necrotrophic phase are hypothesized to be actively attacking the plant cell walls and plant cellular components resulting in necrosis. These genes are being used to develop a new understanding of how this disease interaction progresses and to identify potential targets to reduce the impact of this devastating disease.

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.…”

High-Resolution Transcript Profiling of the Atypical Biotrophic Interaction betweenTheobroma cacaoand the Fungal PathogenMoniliophthora perniciosa

“…We also evaluated the evolutionary pattern of the M. perniciosa CSEPs by performing a comparative analysis with Moniliophthora roreri, a recently sequenced cacao pathogen that is closely related to M. perniciosa (Meinhardt et al, 2014). Using the OrthoMCL program, we defined 11,889 homolog families in these fungi, of which 10,351 had a single gene in each species (orthologs) and 1538 contained more than one gene in at least one of the species (paralogs).…”

“…To evaluate the dN/dS ratio of orthologous genes, all predicted proteins from M. perniciosa, and from its sister species Moniliophthora roreri (Meinhardt et al, 2014), were clustered into homologous families using OrthoMCL (Li et al, 2003) with a minimum BLAST e-value of 1E-5 and inflation index of 1.5. Genes were considered orthologs if clustered in families containing only one copy from each species.…”

Transcriptome and Metabolite Profiling of the Infection Cycle of Zymoseptoria tritici on Wheat Reveals a Biphasic Interaction with Plant Immunity Involving Differential Pathogen Chromosomal Contributions and a Variation on the Hemibiotrophic Lifestyle Definition

“…RNA sequencing (RNAseq) technology has become more frequently used to profile fungal pathogen gene expression at particular phases of plant infection (de Jonge et al, 2012;Kleemann et al, 2012;O'Connell et al, 2012;Soanes et al, 2012;Cantu et al, 2013;Garnica et al, 2013;Hacquard et al, 2013;Meinhardt et al, 2014;Zhang et al, 2014). However, comparatively few studies (Kawahara et al, 2012;Yang et al, 2013;Yazawa et al, 2013) have simultaneously analyzed the responses of both pathogen and host, and very few have undertaken such an analysis throughout a complete pathogen reproductive cycle.…”