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Microb Biotechnol. 2018 Jan;11(1):3-17. doi: 10.1111/1751-7915.13043.

Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement.

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Department of Phytomedicine, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14195, Berlin, Germany.
Hôpital de la Pitié-Salpêtrière, Institute of Cardiometabolism and Nutrition, 47 Boulevard de l'Hôpital, 75013, Paris, France.
School of Biomedical Sciences, Li Kashing Faculty of Medicine, University of Hong Kong, 21 Sassoon Road, Pok Fu Lam, SAR Hong Kong, China.
The Centre for Bacterial Cell Biology, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK.
CEA DRF Genoscope LABGeM, CNRS, UMR8030 Génomique Métabolique, Université d'Evry Val d'Essonne, Université Paris-Saclay, F-91057, Evry, France.
Microbial Evolutionary Genomics Unit, Institut Pasteur, 28 rue du Docteur Roux, 75724, Paris Cedex 15, France.


Genome annotation is, nowadays, performed via automatic pipelines that cannot discriminate between right and wrong annotations. Given their importance in increasing the accuracy of the genome annotations of other organisms, it is critical that the annotations of model organisms reflect the current annotation gold standard. The genome of Bacillus subtilis strain 168 was sequenced twenty years ago. Using a combination of inductive, deductive and abductive reasoning, we present a unique, manually curated annotation, essentially based on experimental data. This reveals how this bacterium lives in a plant niche, while carrying a paleome operating system common to Firmicutes and Tenericutes. Dozens of new genomic objects and an extensive literature survey have been included for the sequence available at the INSDC (AccNum AL009126.3). We also propose an extension to Demerec's nomenclature rules that will help investigators connect to this type of curated annotation via the use of common gene names.

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