De novo sequence assembly of Albugo candida reveals a small genome relative to other biotrophic oomycetesReport as inadecuate




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BMC Genomics

, 12:503

Eukaryote microbial genomics

Abstract

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.

List of abbreviationsNEPNecrosis and Ethylene inducing Peptides

AvrAvirulence

WRRWhite Rust Resistence

CWDCell Wall Degrading

CBELCellulose Binding Elicitor Lectin

CBDCelluslose Binding Domain

ELIElicitin

ELKElicitin Like

HMMHidden Markov Model

tatTwin Arginine Translocase

CRNCrinkler

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-12-503 contains supplementary material, which is available to authorized users.

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Author: Matthew G Links - Eric Holub - Rays HY Jiang - Andrew G Sharpe - Dwayne Hegedus - Elena Beynon - Dean Sillito - Wayne E

Source: https://link.springer.com/article/10.1186/1471-2164-12-503







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