Molecular Mechanisms of Cercospora Pathogenicity Revealed through Comparative Genomics

Members of the fungal genus Cercospora cause devastating foliar diseases of staple crop plants including maize (Zea mays) and soybean (Glycine max).  To date, few genomic resources are available for Cercospora.  The goals of this project were to 1) perform de novo genome sequencing for key members of Cercospora and 2) characterize mechanisms of pathogenicity through comparative and functional genomics.  To this end, we utilized next-generation DNA sequencing technologies (Roche-454, Illumina, and Pacific Biosciences) to obtain genome sequences for C. zeina (pathogen of maize) as well as C. sojina and C. kikuchii (pathogens of soybean).  Genomes were assembled with a hybrid assembly strategy utilizing the SPAdes assembler together with LoRDEC, SSPACE-Standard, SSPACE-LongReads, GapFiller, and PBJelly.  The final C. zeina, C. sojina, and C. kikuchii assemblies resulted in 47.6 Mb, 32.7 Mb, and 33.3 Mb genomes with L50 of 386, 17 and 4, respectively.  Gene prediction analyses were performed with support from RNA sequence data (RNA-Seq) from the three organisms and proteins from closely related species.  Comparative efforts have focused on the identification of genes related to pathogenicity based on the search for secondary metabolite biosynthetic gene clusters, small secreted proteins, carbon-active enzymes, genes potentially undergoing diversifying selection, as well as exclusive and shared genes among Cercospora spp.  This work created novel genomic resources for key Cercospora species impacting global agriculture, and illuminated mechanisms of pathogenesis that are shared among diverse members of the Cercospora.