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Open Access Highly Accessed Research article

De novo sequence assembly of Albugo candida reveals a small genome relative to other biotrophic oomycetes

Matthew G Links12, Eric Holub3, Rays HY Jiang4, Andrew G Sharpe5, Dwayne Hegedus1, Elena Beynon1, Dean Sillito6, Wayne E Clarke17, Shihomi Uzuhashi1 and Mohammad H Borhan1*

Author Affiliations

1 Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK., S7N 0X2 Canada

2 Department of Veterinary Microbiology, 52 Campus Drive, University of Saskatchewan, SK S7N 5B4, Canada

3 School of Life Sciences, University of Warwick, Wellesbourne campus, Wellesbourne, Warwick, CV35 9EF, UK

4 The Broad Institute of MIT and Harvard, Massachusetts 02141, USA

5 National Research Council of Canada - Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada

6 Canadian Intellectual Property Office, Industry Canada, 50 Victoria Street, Gatineau QC, K1A 0C9, Canada

7 Department of Computer Science, 110 Science Place, University of Saskatchewan, Saskatoon, SK S7N 5C9, Canada

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BMC Genomics 2011, 12:503  doi:10.1186/1471-2164-12-503

Published: 13 October 2011

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.

Conclusion

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.