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Background  The  Botryosphaeriaceae  are important plant pathogens, but also have the ability to establish asymptomatic infections that persist for extended periods in a latent state. In this study, we used comparative genome analyses to shed light on the genetic basis of the interactions of these fungi with their plant hosts. For this purpose, we characterised secreted hydrolytic enzymes, secondary metabolite biosynthetic gene clusters and general trends in genomic architecture using all available  Botryosphaeriaceae  genomes, and selected Dothideomycetes genomes.    Results  The  Botryosphaeriaceae  genomes were rich in carbohydrate-active enzymes (CAZymes), proteases, lipases and secondary metabolic biosynthetic gene clusters (BGCs) compared to other Dothideomycete genomes. The genomes of  Botryosphaeria ,  Macrophomina ,  Lasiodiplodia  and  Neofusicoccum,  in particular, had gene expansions of the major constituents of the secretome, notably CAZymes involved in plant cell wall degradation. The  Botryosphaeriaceae  genomes were shown to have moderate to high GC contents and most had low levels of repetitive DNA. The genomes were not compartmentalized based on gene and repeat densities, but genes of secreted enzymes were slightly more abundant in gene-sparse regions.    Conclusion  The abundance of secreted hydrolytic enzymes and secondary metabolite BGCs in the genomes of  Botryosphaeria ,  Macrophomina ,  Lasiodiplodia , and  Neofusicoccum  were similar to those in necrotrophic plant pathogens and some endophytes of woody plants. The results provide a foundation for comparative genomic analyses and hypotheses to explore the mechanisms underlying  Botryosphaeriaceae  host-plant interactions.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07902-w.

bmc genomics

Increased abundance of secreted hydrolytic enzymes and secondary metabolite gene clusters define the genomes of latent plant pathogens in the Botryosphaeriaceae