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

BMC Genomics

Research Article

Elena Beynon¹  Shihomi Uzuhashi¹  Mohammad H Borhan¹  Dwayne Hegedus¹  Wayne E Clarke²  Matthew G Links³  Dean Sillito⁴  Andrew G Sharpe⁵  Eric Holub⁶  Rays HY Jiang⁷ 

[1] Agriculture and Agri-Food Canada, 107 Science Place, S7N 0X2, Saskatoon, SK, Canada;Agriculture and Agri-Food Canada, 107 Science Place, S7N 0X2, Saskatoon, SK, Canada;Department of Computer Science, University of Saskatchewan, 110 Science Place, S7N 5C9, Saskatoon, SK, Canada;Agriculture and Agri-Food Canada, 107 Science Place, S7N 0X2, Saskatoon, SK, Canada;Department of Veterinary Microbiology, University of Saskatchewan, 52 Campus Drive, S7N 5B4, SK, Canada;Canadian Intellectual Property Office, Industry Canada, 50 Victoria Street, K1A 0C9, Gatineau, QC, Canada;National Research Council of Canada - Plant Biotechnology Institute, 110 Gymnasium Place, S7N 0W9, Saskatoon, SK, Canada;School of Life Sciences, University of Warwick, Wellesbourne campus, CV35 9EF, Wellesbourne, Warwick, UK;The Broad Institute of MIT and Harvard, 02141, Massachusetts, USA;

关键词: Bacterial Artificial Chromosome;    Downy Mildew;    Phytophthora Species;    Additional Table;    Estimate Genome Size;   

DOI  :  10.1186/1471-2164-12-503

 received in 2011-06-15, accepted in 2011-10-13,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundAlbugo 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.ResultsA 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.ConclusionAlbugo 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.

【 授权许可】

Unknown   
© Links et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.