title: 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: BACKGROUND
  The 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.
  
  
  RESULTS
  We 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.
  
  
  CONCLUSIONS
  Genome 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.
authors.affiliation: Sustainable Perennial Crops Lab, USDA/ARS, Bldg 001 Rm 223 Beltsville Agricultural Research Center-West, Beltsville, MD 20705, USA. lyndel.meinhardt@ars.usda.gov.
authors.forename: Lyndel W
authors.initials: LW
authors.lastname: Meinhardt
authors.forename: Gustavo Gilson Lacerda
authors.initials: GG
authors.lastname: Costa
authors.forename: Daniela P T
authors.initials: DP
authors.lastname: Thomazella
authors.forename: Paulo José P L
authors.initials: PJ
authors.lastname: Teixeira
authors.forename: Marcelo Falsarella
authors.initials: MF
authors.lastname: Carazzolle
authors.forename: Stephan C
authors.initials: SC
authors.lastname: Schuster
authors.forename: John E
authors.initials: JE
authors.lastname: Carlson
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Guiltinan
authors.forename: Piotr
authors.initials: P
authors.lastname: Mieczkowski
authors.forename: Andrew
authors.initials: A
authors.lastname: Farmer
authors.forename: Thiruvarangan
authors.initials: T
authors.lastname: Ramaraj
authors.forename: Jayne
authors.initials: J
authors.lastname: Crozier
authors.forename: Robert E
authors.initials: RE
authors.lastname: Davis
authors.forename: Jonathan
authors.initials: J
authors.lastname: Shao
authors.forename: Rachel L
authors.initials: RL
authors.lastname: Melnick
authors.forename: Gonçalo A G
authors.initials: GA
authors.lastname: Pereira
authors.forename: Bryan A
authors.initials: BA
authors.lastname: Bailey
mesh_terms: D001482:Base Composition; D001487:Basidiomycota / Q000235:genetics* / Q000378:metabolism*; D002099:Cacao / Q000382:microbiology*; D019295:Computational Biology; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D059646:Genome Size; D016681:Genome, Fungal; D023281:Genomics; D016366:Open Reading Frames; D010935:Plant Diseases / Q000382:microbiology*; D020543:Proteome; D026801:Synteny
chemical_list: D005656:Fungal Proteins; D020543:Proteome