Comparative genomics of maize ear rot pathogens reveals expansion of carbohydrate-active enzymes and secondary metabolism backbone genes in Stenocarpella maydis.

Stenocarpella maydis is a plant pathogenic fungus that causes Diplodia ear rot, one of the most destructive diseases of maize. To date, little information is available regarding the molecular basis of pathogenesis in this organism, in part due to limited genomic resources. In this study, a 54.8 Mb draft genome assembly of S. maydis was obtained with Illumina and PacBio sequencing technologies, and analyzed. Comparative genomic analyses with the predominant maize ear rot pathogens Aspergillus flavus, Fusarium verticillioides, and Fusarium graminearum revealed an expanded set of carbohydrate-active enzymes for cellulose and hemicellulose degradation in S. maydis. Analyses of predicted genes involved in starch degradation revealed six putative α-amylases, four extracellular and two intracellular, and two putative γ-amylases, one of which appears to have been acquired from bacteria via horizontal transfer. Additionally, 87 backbone genes involved in secondary metabolism were identified, which represents one of the largest known assemblages among Pezizomycotina species. Numerous secondary metabolite gene clusters were identified, including two clusters likely involved in the biosynthesis of diplodiatoxin and chaetoglobosins. The draft genome of S. maydis presented here will serve as a useful resource for molecular genetics, functional genomics, and analyses of population diversity in this organism.

Comparison of Stenocarpella maydis Isolates for Isozyme and Cultural Characteristics.

Isolates of Stenocarpella maydis from seed companies and plant disease clinics in the United States and the Republic of South Africa were assayed for isozyme polymorphisms and cultural variability. A low level of isozyme polymorphisms was detected in this collection of isolates. Isozyme polymorphisms were detected for α-esterase, hexose kinase, and malate dehydroge-nase of the enzymes assayed. Fungi often have limited variability among isozyme profiles, and this is especially true for fungi that have host specialization such as biotrophs or fungi with formae speciales designations. Optimum growth temperature, colony color, and pycnidiospore production were also measured. All isolates had an optimum temperature of 28 to 31°C for colony growth on acidified potato dextrose agar. Colony color and pycnidiospore production were variable over the course of several experiments, indicating that these phenotypes are poor genetic markers.