NDLI: The genome sequence and effector complement of the flax rust pathogen Melampsora lini

Content Provider	PubMed Central
Author	Nemri, Adnane Saunders, Diane G. O. Anderson, Claire Upadhyaya, Narayana M. Win, Joe Lawrence, Gregory J. Jones, David A. Kamoun, Sophien Ellis, Jeffrey G. Dodds, Peter N.
Copyright Year	2014
Abstract	Rust fungi cause serious yield reductions on crops, including wheat, barley, soybean, coffee, and represent real threats to global food security. Of these fungi, the flax rust pathogen Melampsora lini has been developed most extensively over the past 80 years as a model to understand the molecular mechanisms that underpin pathogenesis. During infection, M. lini secretes virulence effectors to promote disease. The number of these effectors, their function and their degree of conservation across rust fungal species is unknown. To assess this, we sequenced and assembled de novo the genome of M. lini isolate CH5 into 21,130 scaffolds spanning 189 Mbp (scaffold N50 of 31 kbp). Global analysis of the DNA sequence revealed that repetitive elements, primarily retrotransposons, make up at least 45% of the genome. Using ab initio predictions, transcriptome data and homology searches, we identified 16,271 putative protein-coding genes. An analysis pipeline was then implemented to predict the effector complement of M. lini and compare it to that of the poplar rust, wheat stem rust and wheat stripe rust pathogens to identify conserved and species-specific effector candidates. Previous knowledge of four cloned M. lini avirulence effector proteins and two basidiomycete effectors was used to optimize parameters of the effector prediction pipeline. Markov clustering based on sequence similarity was performed to group effector candidates from all four rust pathogens. Clusters containing at least one member from M. lini were further analyzed and prioritized based on features including expression in isolated haustoria and infected leaf tissue and conservation across rust species. Herein, we describe 200 of 940 clusters that ranked highest on our priority list, representing 725 flax rust candidate effectors. Our findings on this important model rust species provide insight into how effectors of rust fungi are conserved across species and how they may act to promote infection on their hosts.
Related Links	http://dx.doi.org/10.3389/fpls.2014.00098
Starting Page	98
File Format	PDF
ISSN	1664462X
e-ISSN	1664462X
Journal	Frontiers in Plant Science
Volume Number	5
Language	English
Publisher	Frontiers Media S.A.
Publisher Date	2014-03-01
Access Restriction	Open
Rights Holder	Frontiers Media S.A.
Subject Keyword	Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Plant Science

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Components in the haustorial wall of the flax rust fungus,Melampsora lini, are labelled by three anti-calmodulin monoclonal antibodies

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Diversity and Evolution of Effector Loci in Natural Populations of the Plant Pathogen Melampsora lini

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