The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes. The project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of the genes in a single genome. Using the subsystems approach, all of the genes implementing the subsystem are analyzed by an expert in that subsystem. An annotation environment was created where populated subsystems are curated and projected to new genomes. A portable notion of a populated subsystem was defined, and tools developed for exchanging and curating these objects. Tools were also developed to resolve conflicts between populated subsystems. The SEED is the first annotation environment that supports this model of annotation. Here, we describe the subsystem approach, and offer the first release of our growing library of populated subsystems. The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms.

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In an outbreak investigation of Mycobacterium tuberculosis comparing whole genome sequencing (WGS) with traditional genotyping, Stefan Niemann and colleagues found that classical genotyping falsely clustered some strains, and WGS better reflected contact tracing.

The gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria is the causative agent of bacterial spot disease in pepper and tomato plants, which leads to economically important yield losses. This pathosystem has become a well-established model for studying bacterial infection strategies. Here, we present the whole-genome sequence of the pepper-pathogenic Xanthomonas campestris pv. vesicatoria strain 85-10, which comprises a 5.17-Mb circular chromosome and four plasmids. The genome has a high G؉C content (64.75%) and signatures of extensive genome plasticity. Whole-genome comparisons revealed a gene order similar to both Xanthomonas axonopodis pv. citri and Xanthomonas campestris pv. campestris and a structure completely different from Xanthomonas oryzae pv. oryzae. A total of 548 coding sequences (12.2%) are unique to X. campestris pv. vesicatoria. In addition to a type III secretion system, which is essential for pathogenicity, the genome of strain 85-10 encodes all other types of protein secretion systems described so far in gramnegative bacteria. Remarkably, one of the putative type IV secretion systems encoded on the largest plasmid is similar to the Icm/Dot systems of the human pathogens Legionella pneumophila and Coxiella burnetii. Comparisons with other completely sequenced plant pathogens predicted six novel type III effector proteins and several other virulence factors, including adhesins, cell wall-degrading enzymes, and extracellular polysaccharides. Xanthomonas campestris pv. vesicatoria (also designatedXanthomonas axonopodis pv. vesicatoria [101] or Xanthomonas euvesicatoria [46]) is a gram-negative, rod-shaped ␥-proteobacterium with a high genomic GϩC content. Members of the genus Xanthomonas represent an omnipresent group of plantpathogenic bacteria which infect most economically important crop plants and cause a broad variety of diseases (54). X. campestris pv. vesicatoria, the causative agent of bacterial spot disease on pepper (Capsicum spp.) and tomato (Lycopersicon spp.) plants, enters the plant tissue through stomata and wounds. Bacterial colonization of plant intercellular spaces is locally restricted and induces macroscopically visible disease symptoms, so-called water-soaked lesions that later become necrotic (91). The disease results in defoliation and severely spotted fruits, both of which cause massive yield losses. Bacterial spot disease occurs worldwide but is most pernicious in regions with a warm and humid climate.Pathogenicity of X. campestris pv. vesicatoria depends on a type III protein secretion system (TTSS) (11, 17), which is highly conserved among plant and animal pathogenic bacteria (24, 97). In X. campestris pv. vesicatoria, the TTSS is encoded by the chromosomal hrp gene cluster (hypersensitive response and pathogenicity) (11) and translocates effector proteins into the plant cell (96). Once inside the plant cytoplasm, the effectors modulate host cell processes, such as suppression of the plant basal defense mechanisms, for the benefit of the pathog...