Galacturonic acid metabolism in Botrytis cinerea
Pectin is an important component of plant cell walls. Pectin is a complex polymer largely composed of the sugar galacturonic acid. B. cinerea preferentially grows on plant tissues that are rich in pectin, and the production of pectinases is important for B. cinerea to cause disease. All evidence from prior research suggests that pectin is the favorite food for B. cinerea. We study genes involved in galacturonic acid metabolism and their importance for virulence.
Genetic identification of Botrytis resistance loci in Arabidopsis
B. cinerea causes plant tissue rot by secreting a spectrum of pectinases. Infiltration of purified pectinases into plant leaves causes cell wall hydrolysis, tissue collapse and the occurrence of necrosis. Using a genetic screen, we identified a recessive locus in Arabidopsis that confers resistance to damage caused by infiltration with pectinases. The aim of the project is to clone and characterize the gene(s) that confers resistance to B. cinerea pectinases and unravel the resistance mechanism. We hypothesize that plants with resistance to B. cinerea pectinases show (partial) resistance to B. cinerea.
Gene expression in Botrytis cinerea during sexual development
Botrytis cinerea is capable of sexual development in the field. The fruiting body (called ‘apothecium’) can also be produced in the laboratory. Little is known about fungal gene expression in the apothecia and about the genes required for apothecium development. Gene expression in apothecia at different stages of development will be studied using microarray analysis and RT-PCR. The function of selected genes in apothecium development will be studied using targeted mutants.
Comparative genomics of Botrytis species
Recently genome sequences have been determined of 11 species of the genus Botrytis. The raw sequence data are available as short reads of 100 nucleotides. Except for B. cinerea, all Botrytis species have a narrow host range, restricted to a single plant species. We exploit comparative genomics to identify genes that might be involved in determining host specificity. For a thesis project, you can
• Assemble the raw sequence reads to a whole genome assembly
• Compare the quality of the assembly to a reference genome
• Predict gene structures and gene models in an assembly that you made
• Compare the genes in one species with those in other fungi
• Use bio-informatics and evolutionary analyses to identify genes that may be important for host specificity of the fungus that you investigate. This subject is suitable for a BSc or an MSc thesis. It depends on the student’s available time and interests whether all steps described can be accomplished, the project can be divided into smaller subtasks.