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Uncovering these genomic signatures would provide a more reliable method of classification and an increased understanding of host colonization and disease mechanisms, which is of significant importance in developing more effective disease management strategies ( O’Connell et al. Consequently, much research in recent years has focused on establishing the genomic basis underlying differences between species that exhibit different lifestyles. This classification model, which is mainly based on observational data, clearly has limitations, for instance when one species is classified as a necrotroph when interacting with one host but as biotroph when interacting with another ( Veloso and Van Kan 2018). In the same classification model, nonpathogenic species that live within a plant are classified as endophytes, while species that live only on decaying plant material are referred to as saprotrophs. Necrotrophs are characterized as pathogens that feed on dead tissue, biotrophs as pathogens that feed on living tissue, and hemibiotrophs are pathogens that go through an initial biotrophic phase before switching to a necrotrophic phase ( Oliver and Ipcho 2004). Furthermore, these microbes can be linked to 5 different trophic classes based on their specific feeding behavior ( Kabbage et al. they are classified based on their capacity to cause disease symptoms on their host plants. Plant-associated fungi and oomycetes can be broadly classified as pathogens, endophytes, or saprotrophs, i.e. Despite many technological and methodological developments, such as the development of disease-resistant crops, this threat remains a pressing concern for humankind due to emergence of new or adapted species, and a lack of in-depth understanding of disease mechanisms and their genomic basis ( Fudal et al. We thus present the first genomic comparison of multiple citrus-colonizing pathogens and endophytes of the genus Phyllosticta, and therefore provide the basis for further comparative studies into the lifestyle adaptations within this genus.įungal plant pathogens, genomics, CAZymes, lifestyle adaptations, citrus, endophyte, pathogen Introductionįungal and oomycete phytopathogens are a major threat to global food security ( Fisher et al. Phyllosticta citrichinaensis shows an intermediate lifestyle, sharing genomic and phenotypic attributes of both pathogens and endophytes. We also observed that species, based on their carbohydrate active enzymes, group independent of their phylogenetic association, and this clustering correlated with trophy prediction. We found several genomic differences between species of different lifestyles, including groups of genes that were only present in pathogens or endophytes. colonizing Citrus and specifically aimed to elucidate the lifestyle of Phyllosticta citrichinaensis. Here, we examined the genomic differences between pathogenic and endophytic Phyllosticta spp. Furthermore, the lifestyle of Phyllosticta citrichinaensis is ambiguous, as it has been described as a weak pathogen but Koch’s postulates may not have been established and the presence of this species was never reported to cause any crop or economic losses. Thus far, genomic differences underlying lifestyle adaptations of Phyllosticta species have not yet been studied. Some Phyllosticta species have the capacity to cause disease, such as Citrus Black Spot, while others have only been observed as endophytes. Members of the fungal genus Phyllosticta can colonize a variety of plant hosts, including several Citrus species such as Citrus sinensis (orange), Citrus limon (lemon), and Citrus maxima (pomelo).