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

Rainer Borriss (1) , Antoine Danchin (2, 3) , Colin R. Harwood (4) , Claudine Médigue (5) , Eduardo P. C. Rocha (6) , Agnieszka Sekowska (3) , David Vallenet (5)

1 Department of Phytomedicine [Berlin]
2 Li Kashing Faculty of Medicine
3 ICAN - Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases
4 Centre for Bacterial Cell Biology [Newcastle]
5 LABGeM - Analyse Bio-Informatique pour la Génomique et le Métabolisme
6 Génomique évolutive des Microbes / Microbial Evolutionary Genomics

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.

Domaines: Sciences du Vivant [q-bio]

Rainer Borriss, Antoine Danchin, Colin R. Harwood, Claudine Médigue, Eduardo P. C. Rocha, et al.. Bacillus subtilis, the model Gram-positive bacterium: 20years of annotation refinement. Microbial Biotechnology, 2018, 11 (1), pp.3-17. ⟨10.1111/1751-7915.13043⟩. ⟨cea-02291345⟩