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.
Keywords: rust, flax, Melampsora, effector, virulence, avirulence
Citation: Nemri A, Saunders DGO, Anderson C, Upadhyaya NM, Win J, Lawrence GJ, Jones DA, Kamoun S, Ellis JG and Dodds PN (2014) The genome sequence and effector complement of the flax rust pathogen Melampsora lini. Front. Plant Sci. 5:98. doi: 10.3389/fpls.2014.00098
Received: 13 January 2014; Accepted: 28 February 2014;
Published online: 24 March 2014.
Edited by:Sébastien Duplessis, INRA, France
Reviewed by:Pietro Daniele Spanu, Imperial College London, UK
Copyright © 2014 Nemri, Saunders, Anderson, Upadhyaya, Win, Lawrence, Jones, Kamoun, Ellis and Dodds. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Peter N. Dodds, CSIRO Plant Industry, GPO Box 1600, Clunies Ross Street, Canberra, ACT 2601, Australia e-mail: firstname.lastname@example.org