Xanthomonas Whole Genome Sequencing: Phylogenetics, Host Specificity and Beyond

A commentary on Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity Crop diseases impact both yield and product quality and result in important health, economic, environmental, and societal issues worldwide (Scholthof, 2003; Strange and Scott, 2005). These diseases are caused by microorganisms like viruses, fungi, and bacteria. Among phytopathogenic bacteria, the genus Xanthomonas comprises 20 species which together infect more than 400 plant species, among which several important crops such as rice, cassava, cabbages, citrus, or tomato (Mansfield et al., 2012). In contrast, individual Xanthomonas species have a narrow host range usually restricted to a specific plant genus or species. The genetic and molecular bases for host range determination in Xanthomonas are essentially unknown at this date (Jacques et al., 2016): It likely involves bacterial factors enhancing the physiological adaptation to the plant environment (e.g., tropism, attachment, nutrition, degradation of plant compounds) or limiting the elicitation of plant immunity (Büttner and Bonas, 2010). Elicitors of plant immunity include both pathogen-associated molecular patterns (PAMP) and type III effectors (T3E) (Jones and Dangl, 2006). PAMP-triggered immunity (PTI) is the first layer of plant's innate immunity and strongly restricts host range for most bacteria. Key to pathogenicity and host range expansion is pathogen's capacity to suppress PTI. This is the prime function of most T3E known to date. T3E proteins are directly injected inside plant cells using a molecular syringe known as the type III secretion system. As a countermeasure, given T3E might specifically elicit potent immune responses known as effector-triggered immunity (ETI) in a set of plant species resulting in a reduced host range. It is thus key to determine pathogen T3E repertoires. Large scale sequencing of collections of phytopathogenic bacteria at the inter-and intra-specific level has revealed a large diversity of T3E repertoires leading to the definition of core vs. The paper by Schwartz et al. (2015) perfectly illustrates the power of comparative genomics to understand pathogenicity and host specificity of this important genus of pathogens. The authors focussed on bacterial spot disease of tomato and pepper caused by three distinct Xanthomonas species [gardneri (Xg), perforans (Xp), and euvesicatoria (Xe)]. Draft genome sequences were determined for 67 strains sampled in the southeastern and midwestern United States between 1994 and 2013 and subjected to comparative analysis. Importantly, core genome analysis supported the recent reclassification of these strains in three distinct …