Whole genome sequencing of Venturia pirina enables a comparison of effectomes of two fungal fruit pathogens

This thesis investigates the genetic basis of infection and host specificity in the fungal pathogen Venturia pirina. A de novo assembly of the V. pirina genome was used to predict genes thought to be involved in infection and host specificity: “effector” genes; this represents the first genome sequence for this species. Predicted genes in V. pirina were compared to predicted genes in the related species Venturia inaequalis: a species with a similar host, life cycle, and mode of infection, but with different host specificity (V. pirina infects European pear: V. inaequalis infects apple). The suite of effector genes (the “effectome”) was derived for both species using de novo gene prediction programs, identification of secretion motifs, and by identification of known effector motifs. Unique genes for both species were identified, and used as targets in a PCR test designed to distinguish the species for the purposes of biosecurity surveillance. In many cases, gene loss or gene duplication has resulted in a different suite of potential effector genes for each species, which may be the basis of host specificity. Secreted proteins from V. pirina were extracted from an in vitro growth model that is designed to simulate leaf infections, and the presence of secreted proteins inferred by mass spectroscopy and by reference to the genome. This provided in vitro validation for in silico gene predictions. Furthermore, data from mass spectroscopy was used to refine gene predictions for small, secreted proteins that are difficult to predict with current gene prediction methods.

Submission note: A thesis submitted in total fulfilment of the requirements for the degree of Doctor of Philosophy to the Botany Department, School of Life Sciences, Faculty of Science, Technology and Engineering, La Trobe University, Bundoora.