title: De novo sequence assembly of Albugo candida reveals a small genome relative to other biotrophic oomycetes.
abstract: BACKGROUND
  Albugo candida is a biotrophic oomycete that parasitizes various species of Brassicaceae, causing a disease (white blister rust) with remarkable convergence in behaviour to unrelated rusts of basidiomycete fungi.
  
  
  RESULTS
  A recent genome analysis of the oomycete Hyaloperonospora arabidopsidis suggests that a reduction in the number of genes encoding secreted pathogenicity proteins, enzymes for assimilation of inorganic nitrogen and sulphur represent a genomic signature for the evolution of obligate biotrophy. Here, we report a draft reference genome of a major crop pathogen Albugo candida (another obligate biotrophic oomycete) with an estimated genome of 45.3 Mb. This is very similar to the genome size of a necrotrophic oomycete Pythium ultimum (43 Mb) but less than half that of H. arabidopsidis (99 Mb). Sequencing of A. candida transcripts from infected host tissue and zoosporangia combined with genome-wide annotation revealed 15,824 predicted genes. Most of the predicted genes lack significant similarity with sequences from other oomycetes. Most intriguingly, A. candida appears to have a much smaller repertoire of pathogenicity-related proteins than H. arabidopsidis including genes that encode RXLR effector proteins, CRINKLER-like genes, and elicitins. Necrosis and Ethylene inducing Peptides were not detected in the genome of A. candida. Putative orthologs of tat-C, a component of the twin arginine translocase system, were identified from multiple oomycete genera along with proteins containing putative tat-secretion signal peptides.
  
  
  CONCLUSIONS
  Albugo candida has a comparatively small genome amongst oomycetes, retains motility of sporangial inoculum, and harbours a much smaller repertoire of candidate effectors than was recently reported for H. arabidopsidis. This minimal gene repertoire could indicate a lack of expansion, rather than a reduction, in the number of genes that signify the evolution of biotrophy in oomycetes.
authors: Agriculture and Agri-Food Canada, Saskatoon, SK, S7N 0X2 Canada.
authors: Matthew G
authors: MG
authors: Links
authors: Eric
authors: E
authors: Holub
authors: Rays H Y
authors: RH
authors: Jiang
authors: Andrew G
authors: AG
authors: Sharpe
authors: Dwayne
authors: D
authors: Hegedus
authors: Elena
authors: E
authors: Beynon
authors: Dean
authors: D
authors: Sillito
authors: Wayne E
authors: WE
authors: Clarke
authors: Shihomi
authors: S
authors: Uzuhashi
authors: Mohammad H
authors: MH
authors: Borhan
mesh_terms: D000595:Amino Acid Sequence; D019607:Brassicaceae / Q000469:parasitology; D020224:Expressed Sequence Tags; D005656:Fungal Proteins / Q000737:chemistry / Q000378:metabolism; D016678:Genome; D008969:Molecular Sequence Data; D009868:Oomycetes / Q000235:genetics*; D010935:Plant Diseases / Q000469:parasitology; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA
chemical_list: D005656:Fungal Proteins