Discovery and genomic architecture of Cercospora zeina (Crous & U. Braun) effector genes

Abstract

In Africa, the grey leaf spot disease in maize is caused by the hemibiotrophic Dothideomycete Cercospora zeina. Dothideomycetes consist of many economically important phytopathogenic fungi. During infection of the host, phytopathogenic fungi secrete effectors that promote infection. In this dissertation, I review how various effectors perform their function. I then review how the “two-speed” genome of many Dothideomycete phytopathogens is important for the gain of virulence and loss of avirulence effector genes in the constant molecular arms race with the plant host. Furthermore, to improve our understanding of the pathogenicity of C. zeina, we aim to identify the effector gene catalogue and analyse its genome architecture. We present a contiguous genome assembly of C. zeina generated by PacBio SMRT sequencing technology. The assembly consists of 17 nuclear genome contigs that make up the 41 Mbp genome and contain three possible full chromosomes. The annotation of the genome has revealed a secretome that contains many proteins predicted to have oxidoreductive and peroxidase activities. Effector prediction revealed a total of 274 effectors which included potential homologues of the ECP2, ECP6 and AVR4 effectors from Cladosporium fulvum. These results imply that C. zeina potentially secretes proteins that prevent recognition by the host and protect against oxidative stress. Additionally, genome architecture analysis of C. zeina has revealed a bipartite structure consisting of 33.2% AT-rich compartments and 66.8% GC-rich compartments. However, effector genes are not concentrated in the AT-rich compartments. This study has paved way for the functional characterization of candidate C. zeina effectors which could ultimately lead to effector-based breeding of maize.