Genomes and transcriptomes of partners in plant-fungal-interactions between canola (Brassica napus) and two Leptosphaeria species

PLoS One. 2014 Jul 28;9(7):e103098. doi: 10.1371/journal.pone.0103098. eCollection 2014.


Leptosphaeria maculans 'brassicae' is a damaging fungal pathogen of canola (Brassica napus), causing lesions on cotyledons and leaves, and cankers on the lower stem. A related species, L. biglobosa 'canadensis', colonises cotyledons but causes few stem cankers. We describe the complement of genes encoding carbohydrate-active enzymes (CAZys) and peptidases of these fungi, as well as of four related plant pathogens. We also report dual-organism RNA-seq transcriptomes of these two Leptosphaeria species and B. napus during disease. During the first seven days of infection L. biglobosa 'canadensis', a necrotroph, expressed more cell wall degrading genes than L. maculans 'brassicae', a hemi-biotroph. L. maculans 'brassicae' expressed many genes in the Carbohydrate Binding Module class of CAZy, particularly CBM50 genes, with potential roles in the evasion of basal innate immunity in the host plant. At this time, three avirulence genes were amongst the top 20 most highly upregulated L. maculans 'brassicae' genes in planta. The two fungi had a similar number of peptidase genes, and trypsin was transcribed at high levels by both fungi early in infection. L. biglobosa 'canadensis' infection activated the jasmonic acid and salicylic acid defence pathways in B. napus, consistent with defence against necrotrophs. L. maculans 'brassicae' triggered a high level of expression of isochorismate synthase 1, a reporter for salicylic acid signalling. L. biglobosa 'canadensis' infection triggered coordinated shutdown of photosynthesis genes, and a concomitant increase in transcription of cell wall remodelling genes of the host plant. Expression of particular classes of CAZy genes and the triggering of host defence and particular metabolic pathways are consistent with the necrotrophic lifestyle of L. biglobosa 'canadensis', and the hemibiotrophic life style of L. maculans 'brassicae'.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Ascomycota / genetics*
  • Brassica napus / genetics*
  • Brassica napus / microbiology*
  • Cluster Analysis
  • Cotyledon / genetics
  • Cotyledon / microbiology
  • Gene Expression Regulation, Fungal
  • Gene Expression Regulation, Plant
  • Genome, Fungal*
  • Genome, Plant*
  • Genomics
  • Host-Pathogen Interactions / genetics*
  • Peptide Hydrolases / chemistry
  • Peptide Hydrolases / genetics
  • Phenotype
  • Plant Diseases / genetics
  • Plant Diseases / microbiology
  • Transcriptome*


  • Peptide Hydrolases

Grant support

The following sources of funding supported this work: Grains Research and Development Corporation for funding RL AW BC BH, the Australian Research Council for funding AC, the Victoria Life Sciences Computation Initiative (VLSCI) for computational resources via grant RAS990 for RL, the University of Melbourne for an Early Career Researcher award to RL, and the French agency Agence Nationale de la Recherche, contract ANR-09-GENM-028 (‘FungIsochores’) for funding JG and TR. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.