A novel phyllosphere residentProtomycesspecies that interacts with theArabidopsisimmune system

Abstract

We describe the genome contents of six Protomyces spp. that are pathogenic within the typical host range of the genus and a novel Protomyces strain (SC29) that was previously isolated from the phylloplane of wild Arabidopsis thaliana (Arabidopsis), an atypical or possible alternate host. Genome-wide phylogenetic analysis defined SC29 as a distinct Protomyces sp. Analysis of gene family expansions, gene retention, and gene loss patterns among these Protomyces spp. lead us to hypothesize that SC29 may have undergone a host jump. The role of phyllosphere residency in the lifecycle of Protomyces spp. was previously unknown. Genomic changes in SC29 and all other Protomyces spp. were consistent with adaptations to the plant phylloplane. As predicted by our analysis of its mating locus, SC29 did not cause disease on Arabidopsis as a single strain, but could persist in its phylloplane, while the closely related P. inouyei does not. SC29 treated Arabidopsis exhibited enhanced immunity against Botrytis cinerea infection, associated with activation of MAPK3/6, camalexin, and SA-signalling pathways. We conclude that SC29 is a novel Protomyces sp. able to survive in the Arabidopsis phylloplane and that phylloplane residency is an important element in the lifecycle of Protomyces spp.

A novelArabidopsisphyllosphere residentProtomycessp. and a re-examination of genusProtomycesbased on genome sequence data

“…The isolation and culture Protomyces SC29 from the leaf surface of healthy wildgrowing Arabidopsis thaliana (Arabidopsis), in Helsinki, Finland, were described in our previous study, Wang et al (Wang et al 2016). DNA extraction, PCR amplification or marker sequences, and DNA sequencing, were described in our previous studies (Wang et al 2019;Wang et al 2016). Average nucleotide identity (ANI) and average amino-acid identity (AAI) values of Protomyces genomes or proteomes were calculated using online tool ANI/AAI-Matrix (Rodriguez-R and Konstantinidis 2016).…”

“…Average nucleotide identity (ANI) and average amino-acid identity (AAI) values of Protomyces genomes or proteomes were calculated using online tool ANI/AAI-Matrix (Rodriguez-R and Konstantinidis 2016). Growth assays at low temperature were previously reported in (Wang et al 2019). Yeast cell size and morphological characterization was conducted by photographing three-day-old or two-week-old cultures with a LEICA 2500 microscope (www.leica-microsystems.com) or two-week-old colonies with a LEICA MZ10F stereo microscope.…”

“…LT602858) showing highest similarity (96 %) to P. inouyei (Wang et al 2016). The SC29 genome and the genomes of six reference species were previously sequenced and subjected to comparative analysis (Wang et al 2019). These six sequenced species represent all of the Protomyces species, for which strains are currently available in yeast culture collections ( Table 1).…”

“…have small genome sizes (11.5-14.1 Mbp) with 50.9-52.8 % GC content. Our previous work (Wang et al 2019) focused on the basic description of SC29, its interactions with Arabidopsis, and comparison of the features of the seven sequenced genomes. In the current work, we focus on the description and naming of SC29 as a novel species as well as the phylogenetic implications of our Protomyces genome sequencing results (Wang et al 2019).…”

“…It has been suggested that members of the genus Protomyces, its sister genus Taphrina, and some other members of the order Taphrinales, may have retained the lifestyles of early Ascomycetes, due their many ancestral features and basidiomycete-like traits, such as high genomic GC content (Sugiyama et al 1996;Wang et al 2019), thick walled "chlamydospore" reproductive or resting cells (Bary and Garnsey 1887;Mix 1924), basidiospore-like naked asci (Sadebeck 1884;Lohwag 1934), enteroblastic budding pattern (Sugiyama et al 1996; Von Arx and Weijman 1979) Q-10 ubiquinone system (Sugiyama et al 2006), and the presence of a dual hybrid histidine kinase (Wang et al 2019). These similarities are also illustrated by the many instances, in which species within the order Taphrinales have been misclassified among the Basidiomycetes, or vice versa (Piepenbring and Bauer 1997;Bary and Garnsey 1887;Reddy and Kramer 1975;Nishida and Sugiyama 1995).…”