Genome assembly, annotation and comparative analysis of the maize fungal pathogen Cercospora zeina

Abstract

The fungal pathogen Cercospora zeina causes Grey leaf spot (GLS), a devastating yield-limiting foliar disease of maize. GLS negatively impacts food security, especially in sub-Saharan Africa where maize is a staple food source. In this study the genomic DNA of C. zeina was sequenced using next-generation sequencing, and the genome assembled to a 95.4% completeness based on the presence of core genes. The functionality of the genome was confirmed by transcriptome sequencing data mapping to the genome. Phylogenetics analysis confirmed the genome to cluster with other C. zeina isolates. The functional elements and gene regions were predicted using the MAKER genome annotation pipeline. The predicted proteins were compared with the closely related species Cercospora zeae-maydis, Cercospora beticola and Cercospora berteroae. Functional annotation of proteins of specific classes were performed to identify differences in secreted proteins, carbohydrate-active enzymes, lipases, proteases and components of secondary metabolite biosynthesis clusters. The synteny of the genes in the cercosporin toxin biosynthesis cluster was also confirmed in all four species. To enhance the accuracy of the phylogenetic classification of Cercospora species the orthologous relationship between proteins of a number of Dothideomycete species were predicted. The single-copy orthologs specific to the Cercospora genus were analyzed for phylogenetic information content, and eight genes selected for primer design in regions of protein identity. Primers for four genes were synthesized and tested for specificity during amplification of C. zeina and C. zeae-maydis genomic DNA. Degenerate primer pairs for two genes were selected for further analysis, due to sequencing confirming the correct identity of the amplification products.