Enemy or ally: a genomic approach to elucidate the lifestyle of Phyllosticta citrichinaensis

Author:

Buijs Valerie A12ORCID,Groenewald Johannes Z1ORCID,Haridas Sajeet3ORCID,LaButti Kurt M3ORCID,Lipzen Anna3ORCID,Martin Francis M4ORCID,Barry Kerrie3ORCID,Grigoriev Igor V35ORCID,Crous Pedro W12ORCID,Seidl Michael F6ORCID

Affiliation:

1. Evolutionary Phytopathology, Westerdijk Fungal Biodiversity Institute , Utrecht 3584 CT , The Netherlands

2. Department of Plant Sciences, Laboratory of Phytopathology, Wageningen University and Research , Wageningen 6708 PB , The Netherlands

3. US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley , CA 94720, USA

4. Department of Biology, Institut National de la Recherche Agronomique, UMR INRA-Université de Lorraine “Interaction Arbres/Microorganismes” , Champenoux F-54280, France

5. Department of Plant and Microbial Biology, University of California Berkeley , Berkeley, CA 94720, USA

6. Theoretical Biology & Bioinformatics, Utrecht University , Utrecht 3584 CH , The Netherlands

Abstract

Abstract 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). Some Phyllosticta species have the capacity to cause disease, such as Citrus Black Spot, while others have only been observed as endophytes. Thus far, genomic differences underlying lifestyle adaptations of Phyllosticta species have not yet been studied. 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. Here, we examined the genomic differences between pathogenic and endophytic Phyllosticta spp. colonizing Citrus and specifically aimed to elucidate the lifestyle of Phyllosticta citrichinaensis. We found several genomic differences between species of different lifestyles, including groups of genes that were only present in pathogens or 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. Phyllosticta citrichinaensis shows an intermediate lifestyle, sharing genomic and phenotypic attributes of both pathogens and endophytes. 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.

Funder

Dutch Applied Science division (TTW) of NWO and the Technology Program of the Ministry of Infrastructure and Water Management

Research Programme I&W Biotechnology and Safety

U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy

Publisher

Oxford University Press (OUP)

Subject

Genetics (clinical),Genetics,Molecular Biology

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