Open AccessBacillus subtilis, the model Gram‐positive bacterium: 20 years of annotation refinement
Author(s) -
Borriss Rainer,
Danchin Antoine,
Harwood Colin R.,
Médigue Claudine,
Rocha Eduardo P.C.,
Sekowska Agnieszka,
Vallenet David
Publication year - 2018
Publication title -
microbial biotechnology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.287
H-Index - 74
ISSN - 1751-7915
DOI - 10.1111/1751-7915.13043
Subject(s) - annotation , genome , gene annotation , whole genome sequencing , bacillus subtilis , genome project , computational biology , genomics , dna sequencing , biology , computer science , genetics , gene , bacteria
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 AL 009126.3). 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.