CSIRO Homepage Flax Rust Genomic Resources

Melampsora lini infection of flax

Rust fungi are one of the largest and most destructive groups of plant pathogens. They are obligate biotrophs which require a living host for survival. Melampsora lini, the causal agent of flax rust, has long been recognized as a model system for studying host-pathogen interactions (Flor, 1955). Like many other rusts, the 189 Mb genome of Melampsora lini is dramatically expanded and riddled with transposable elements (Nemri et al., 2014).

Please cite the following publication(s) if you use the data from this genome in your research:

Nemri A, Saunders DG, Anderson C, Upadhyaya NM, Win J, Lawrence GJ, Jones DA, Kamoun S, Ellis JG, Dodds PN (2014) The genome sequence and effector complement of the flax rust pathogen Melampsora lini. Front Plant Sci. 2014 Mar 24;5:98. doi: 10.3389/fpls.2014.00098

Additional references:
Flor, H. H. (1955). Host-parasite interaction in flax rust - its genetics and other implications. Phytopathology 45, 680-685

Link to: genome browser  as <demo> user and <pass> password  or as <Guest> user and no password 

Link to downloads:
CH5_v5_reference  fasta file (tar.gz) of the current version of de novo assembled genome of flax rust pathogen isolate CH5 (21,310 scaffolds).

CH5_v5_reference_repeatmasked  fasta file (tar.gz) repeat masked genome.

CH5_v5_EVM_unfiltered_set   Annotation (gff3), gene (fasta),transcripts (fasta), CDS (fasta), protein (fasta) files of complete set (32,859) of  transcription unit models predicted by Evidence Modeler Evidences included assembled transcripts from RNAseq and haustorial specific ESTs (Cufflinks, Trinity), spliced protein-to-genome alignments (Exonerate) using Mlp and Pgt proteomes, ab initio gene predictions (Augustus, GeneMark-es). This set includes protein-coding genes, transposable elements, pseudogenes (predicted proteins < 50 aa, those missing start codon and possible alternate splice forms.

CH5_v5_EVM_filtered_set  Annotation (gff3), transcripts (fasta), CDS (fasta), protein (fasta) files of 16,339 protein-coding genes (one best model per locus).

Link to:  M. lini  page at Joint Genome Institute (JGI) fungal genome Resource MycoCosm


Adnane Nemri
Narayana Upadhyaya 
Jeff Ellis
Peter Dodds