Bacillus subtilis, the model Gram‐positive bacterium: 20 years of annotation refinement. Issue 1 (26th December 2017)

• Record Type: Journal Article
• Authors: Borriss, Rainer; Danchin, Antoine; Harwood, Colin R.; Médigue, Claudine; Rocha, Eduardo P.C.; Sekowska, Agnieszka; Vallenet, David
• Other Names: Aulenta Federico guestEditor.; Harnisch Falk guestEditor.; Puig Sebastià guestEditor.
• Is Part Of: Microbial biotechnology. Volume 11:Issue 1(2018:Jan.)
• Page Start: 3
• Page End: 17
• Publication Date: 2017-12-26
• Subjects: Microbial biotechnology -- Periodicals; Biotechnology; Microbiology; 660.62
• DOI: 10.1111/1751-7915.13043
• Languages: English
• ISSNs: 1751-7915

Abstract

Summary: 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. Abstract : Steering life of a model Firmicute, the Bacillus subtilis genome comprises all the genes of the minimal AT‐rich genome (the paleome). Within an epiphytic organism its cenome's genes sense light and scavenge plant fibers and metabolites. Making a differentiating organism the genome codes for spores and biofilms (the histome).