Leptosphaeria maculans genome project

Leptosphaeria maculans 'brassicae' (Lmb) is the ascomycete fungus that causes "stem canker" (also termed "Blackleg") on oilseed rape, Brassica napus, and numerous other crucifers [3]. It is representative of an important genus of fungal phytopathogens, the Dothideomycetes, of which six other species have been, or are in the process of being, sequenced by US sequencing centers. The life cycle of Lmb is extremely complex and includes alternate phases of saprophytism on stem residues, necrotrophy on leaves, endophytism within plant tissues and necrotrophy at the basis of the stem [3]. The disease is endemic in all oilseed rape-growing parts of the world and may cause 5-20% average yield losses due to lodging of the crop before harvest. Lmb develops gene-for-gene interactions with its host plants and is considered as a model to study specificity of interaction and adaptation to plant resistance gene selection pressure in agro-ecosystems [3,7]

The genome initiative for Leptosphaeria maculans 'brassicae' was launched in 2004 and led by T. Rouxel, M.H. Balesdent (INRA-Bioger) and B.J. Howlett (University of Melbourne, Australia). It was strongly supported by the "Dothideomycete" scientific community and industry, including seed companies involved in the oilseed rape market. The genome was sequenced by the French sequencing center, Genoscope. The first assembly was provided in January 2007, followed by a refined second assembly in August 2007. The structural and functional annotations are in progress.

Objectives

• Genome sequencing
• Structural annotation
  • Gene prediction
  • Transposable element annotation
• Functional annotation
• Manual curation
• Comparative genomics

First genome facts

• Mitochondrial genome is 155 kb, which is significantly larger than that of other dothideomycetes.
• The current assembly is of high quality comprising 76 supercontigs with 50% of the genome in only 9 scaffolds bigger than 1.8 Mb. The mitochondrial genome and a probable minichromosome also occur as a single scaffold.
• The first ab initio step of the structural annotation pipeline (Fgenesh processed with Leptosphaeria parameters) has predicted 9342 genes.
• In addition to preliminary studies on Lmb transposable elements [1], a Transposable Element pipeline has been used for the detection (TEdenovo) and the annotation (TEannot) of transposable elements in L. maculans genome sequences and the families of repeats thus identified currently manually expertised. A GnpGenome instance has been set up for Lmb Structural annotation and available secure access

Post-genomic approaches results

To validate the current assembly and facilitate further map-based cloning strategies, efforts are focused on the generation of a physical map linking the available genetic map and the genome sequence. The very high level of meiotic recombination within chromosomes necessitates that novel mini or microsatellite-type markers are generated for this purpose [2].

Comparative genomics approaches are underway with the genome of Stagonospora nodorum (R. Oliver, Murdoch University, Australia) to evaluate gene conservation, synteny and repeated elements history. A Dothideomycete comparative platform is being set-up at the JGI (USA) and should enable expansion of these studies.

A specific focus is on the annotation and analysis of small-secreted proteins possibly acting as effectors [4,6]. Within the framework of the French Research Agency ANR-funded project FungEffector (led by M.H. Lebrun, INRA-Bioger), bioinformatics, transcriptomics and proteomics approaches are being developed for this purpose.