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

Rainer Borriss,Antoine Danchin,Eduardo P C Rocha,Colin R Harwood,Claudine Médigue,David Vallenet,Agnieszka Sekowska

doi:10.1111/1751-7915.13043

Abstract

SummaryGenome 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.

Highlights

With the advent of Generation Sequencing (NGS) techniques, sequencing genomes has become routine
Strain 168 remains a case in point, and here we present an updated annotation, based on experimental evidence collected for this organism and from other organisms, that we describe here with the aim of summarizing knowledge about this bacterium as a possible chassis for Synthetic Biology studies
Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology., Microbial Biotechnology, 11, 3–17

Summary

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. 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 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

Introduction

Conclusions

Findings

Conflict of interest