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Repeated Gain and Loss of a Single Gene Modulates The SCIENCE ADVANCES | RESEARCH ARTICLE EVOLUTIONARY BIOLOGY Copyright © 2020 The Authors, some rights reserved; Repeated gain and loss of a single gene modulates exclusive licensee American Association the evolution of vascular plant pathogen lifestyles for the Advancement Emile Gluck-Thaler1,2*, Aude Cerutti3*, Alvaro L. Perez-Quintero4*, Jules Butchacas1,5, of Science. No claim to 1,5 6 7 7 original U.S. Government Verónica Roman-Reyna , Vishnu Narayanan Madhavan , Deepak Shantharaj , Marcus V. Merfa , Works. Distributed 8,9,10 11 8,9 4 12 Céline Pesce , Alain Jauneau , Taca Vancheva , Jillian M. Lang , Caitilyn Allen , under a Creative 8 8 8 13 7 Valerie Verdier , Lionel Gagnevin , Boris Szurek , Gregg T. Beckham , Leonardo De La Fuente , Commons Attribution Hitendra Kumar Patel6, Ramesh V. Sonti6, Claude Bragard9, Jan E. Leach4, Laurent D. Noël3, License 4.0 (CC BY). Jason C. Slot1,5, Ralf Koebnik8†, Jonathan M. Jacobs1,5† Vascular plant pathogens travel long distances through host veins, leading to life-threatening, systemic infec- tions. In contrast, nonvascular pathogens remain restricted to infection sites, triggering localized symptom devel- opment. The contrasting features of vascular and nonvascular diseases suggest distinct etiologies, but the basis for each remains unclear. Here, we show that the hydrolase CbsA acts as a phenotypic switch between vascular and nonvascular plant pathogenesis. cbsA was enriched in genomes of vascular phytopathogenic bacteria in the family Xanthomonadaceae and absent in most nonvascular species. CbsA expression allowed nonvascular Xanthomonas to cause vascular blight, while cbsA mutagenesis resulted in reduction of vascular or enhanced nonvascular symptom development. Phylogenetic hypothesis testing further revealed that cbsA was lost in mul- tiple nonvascular lineages and more recently gained by some vascular subgroups, suggesting that vascular pathogenesis is ancestral. Our results overall demonstrate how the gain and loss of single loci can facilitate the evolution of complex ecological traits. INTRODUCTION plant pathogenic and commensal Pseudomonas (5), transitions Pathogenic microorganisms cause diseases of animals and plants. between mutualist and parasitic phenotypes in nitrogen-fixing bac- Some pathogenic species colonize the host vasculature, which leads teria (6, 7), and transitions between mutualistic and plant patho- to systemic infection, while others remain localized to nonvascular genic Rhodococcus (8) have all been shown to reproducibly occur tissues. Complex structural and biochemical differences between through the gain and loss of genomic islands containing multiple vascular and nonvascular tissues suggest that pathogens have mul- genes all contributing to the same phenotype. These rapid evolu- tiple distinct adaptations to either environment, yet the genetic and tionary dynamics have profound implications for our understanding evolutionary bases of these adaptations are largely unknown. of disease ecology and disease management strategies. Adaptations often occur through wholesale gain and loss of In plants, vascular xylem and nonvascular parenchyma tissues specific genes, resulting in more rapid evolution compared with represent distinct niches. Xylem is composed of dead cells with incremental changes at the DNA sequence level alone (1). In bacteria, highly reinforced walls organized into cylinders that provide plants gene gain occurs primarily through horizontal gene transfer (HGT), with structural integrity and a means of long-distance fluid trans- while gene loss or pseudogenization occurs through multiple mech- port. In contrast, parenchyma tissues are composed of living cells anisms, including transposon-mediated insertions and sequence and gas-filled intercellular spaces. Xylem fluid consists primarily of deletions in open reading frames (2–4). Especially for loci encoding water and mineral nutrients, and many vascular pathogens success- ecologically relevant traits, gene gain and loss effectively act as phe- fully colonize this plant environment (9). Xylem tissue not only notypic switches, enabling rapid shifts between what otherwise runs throughout the plant, enabling the distribution of water from seem like complex lifestyles (3). For example, transitions between roots to leaves, but also serves as a potential pathway for rapid, sys- temic transport of pathogens. The gammaproteobacterial family Xanthomonadaceae includes 1Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, two major genera, Xanthomonas and Xylella, that cause vascular USA. 2Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, diseases of plants. Bacteria in the genus Xylella are fastidious, insect- USA. 3LIPM, Université de Toulouse, INRAE, CNRS, Université Paul Sabatier, Castanet- vectored vascular pathogens. Xanthomonas is a diverse genus of 4 Tolosan, France. Agricultural Biology, Colorado State University, Fort Collins, CO, plant-associated Gram-negative bacterial species that cause vascu- USA. 5Infectious Disease Institute, The Ohio State University, Columbus, OH 43210, USA. 6CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India lar and nonvascular diseases of more than 350 monocot and dicot 7Department of Entomology and Plant Pathology, Auburn University, Auburn, AL plant hosts (10). Xanthomonas species are separated into subgroups 8 9 36849, USA. IRD, CIRAD, Université Montpellier, IPME, Montpellier, France. Earth & Life called pathovars (pv.) based on their phenotypic behavior such as Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium. 10HM Clause (Limagrain group), Davis, CA, 95618, USA. 11Institut Fédératif de Recherche symptom development (e.g., vascular or nonvascular) or host range 3450, Plateforme Imagerie, Pôle de Biotechnologie Végétale, Castanet- Tolosan, (10). Vascular xanthomonads invade the water-transporting xylem; France. 12Department of Plant Pathology, University of Wisconsin–Madison, Madison, 13 nonvascular Xanthomonas species cause localized symptoms by WI 53706, USA. Renewable Resources and Enabling Sciences Center, National Renewable colonizing the mesophyll. Although often closely related, the genetic Energy Laboratory, Golden, CO 80401, USA. *These authors contributed equally to this work. determinants distinguishing vascular from nonvascular Xanthomonas †Corresponding author. Email: [email protected] (J.M.J.); [email protected] (R.K.) lineages at the intraspecific level are not clear. Gluck-Thaler et al., Sci. Adv. 2020; 6 : eabc4516 13 November 2020 1 of 10 SCIENCE ADVANCES | RESEARCH ARTICLE Here, we used Xanthomonas as a model to study the etiology of lifestyles were dependent on that OG’s presence or absence using plant vascular pathogenesis because this genus contains multiple BayesTraitsV3 (Fig. 1) (11). The phylogenetic relationships between independent pairs of strains from the same species (i.e., pathovars) vascular and nonvascular pathovars indicated that xylem pathogen- that cause either vascular or nonvascular diseases. This enabled us esis is paraphyletic, i.e., not limited to a single clade, an individual to disentangle genetic features that are shared due to ancestry and Xanthomonas sp., or host plant genus (Fig. 1 and figs. S1 and S2). those that may be shared due to common tissue-specific lifestyles. Instead, vascular diseases of many host plant families are caused by Given the tendency of bacteria to evolve through the gain and loss different pathovars across the Xanthomonas genus. We identified of genes organized into clusters or genomic islands, we hypothe- two OGs whose presence was strongly associated with the distribu- sized that vascular and nonvascular pathogenesis emerge through tion of tissue-specific lifestyles (Fig. 1, fig. S1, and tables S1 and S2). the gain and loss of small numbers of linked loci. We found evi- One OG (OG0003492, log Bayes factor = 15.19) was highly associ- dence supporting the most extreme version of this hypothesis, ated with vascular pathogenesis, while the other (OG0002818, log where transitions between vascular and nonvascular lifestyles are Bayes factor = 10.51) was associated with nonvascular pathogenesis. mediated by the repeated gain and loss of a single gene that acts as a For this study, we focused on vascular pathogen-enriched OG0003492, phenotypic switch. which encodes a cell wall–degrading cellobiohydrolase (EC 3.2.1.4, glycosylhydrolase family GH6) called CbsA (12, 13). CbsA was present in all taxa classified as vascular with one RESULTS exception (Xanthomonas hortorum) and was absent from most cbsA is significantly associated with vascular pathogenesis nonvascular taxa. CbsA was also found in some strains with unde- We first identified high-priority candidate genes associated with termined tissue specificity due to unavailable or conflicting infor- transitions to vascular and nonvascular lifestyles. We classified mation in the literature (table S1). Phylogenetic analysis of CbsA annotated proteins from 59 publicly available whole-genome se- sequences revealed that within Xanthomonas, CbsA sequences form quences of plant pathogenic Xanthomonadaceae bacteria in the two major clades: the first contains sequences found in vascular, Xanthomonas and Xylella genera into ortholog groups (OGs). We then nonvascular (or undetermined) pathogen genomes (found in type 3 conducted an analysis of trait evolution across a single-nucleotide neighborhood in Fig. 1B; see below), and the second contains se- polymorphism (SNP)–based
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