1887

Abstract

Comparative genomics is the cornerstone of identification of gene functions. The immense number of living organisms precludes experimental identification of functions except in a handful of model organisms. The bacterial domain is split into large branches, among which the Firmicutes occupy a considerable space. has been the model of Firmicutes for decades and its genome has been a reference for more than 10 years. Sequencing the genome involved more than 30 laboratories, with different expertises, in a attempt to make the most of the experimental information that could be associated with the sequence. This had the expected drawback that the sequencing expertise was quite varied among the groups involved, especially at a time when sequencing genomes was extremely hard work. The recent development of very efficient, fast and accurate sequencing techniques, in parallel with the development of high-level annotation platforms, motivated the present resequencing work. The updated sequence has been reannotated in agreement with the UniProt protein knowledge base, keeping in perspective the split between the paleome (genes necessary for sustaining and perpetuating life) and the cenome (genes required for occupation of a niche, suggesting here that is an epiphyte). This should permit investigators to make reliable inferences to prepare validation experiments in a variety of domains of bacterial growth and development as well as build up accurate phylogenies.

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2009-06-01
2019-11-20
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tRNAs series observed in the original sequence of 168. The upper part reports tRNA series found in rDNA cluster spacers, whereas the lower part shows those that are found elsewhere on the chromosome. Subseries that are shared by several clusters are indicated by coloured boxes. The triad specific to the triple cluster rDNA I, H and G is indicated in a red box. [ Excel file] (36 kb) Syntactic feature updates in the 168 new genome sequence. The table identifies (comparing with the previously available sequence and annotation of B. subtilis 168): 1, new genes; 2, sequence corrections which resulted in gene fusion or fission; 3, genes with N-terminal and C-terminal variations in the protein sequences; 4, genes with amino acid variations in their core sequence. [ Excel file] (146 kb) Regions of genomic plasticity in the genome of 168. Regions predicted by MaGe are marked in brown when also containing genomic island signatures, and in blue otherwise. Predictions not seen using MaGe are marked in green. Phage regions are highlighted in yellow. The predicted genomic regions are marked with 'Y' when they have been described previously. [ Excel file] (73 kb) Correspondence analysis of the amino acid distribution in the proteome of 168. The table lists the proteins according to their belonging to the integral inner-membrane (IIMP) class or to the bulk protein class. A reliability factor tells whether ascribing a protein to class I or class II has a strong relevance or not. [ Excel file] (567 kb)

EXCEL

tRNAs series observed in the original sequence of 168. The upper part reports tRNA series found in rDNA cluster spacers, whereas the lower part shows those that are found elsewhere on the chromosome. Subseries that are shared by several clusters are indicated by coloured boxes. The triad specific to the triple cluster rDNA I, H and G is indicated in a red box. [ Excel file] (36 kb) Syntactic feature updates in the 168 new genome sequence. The table identifies (comparing with the previously available sequence and annotation of B. subtilis 168): 1, new genes; 2, sequence corrections which resulted in gene fusion or fission; 3, genes with N-terminal and C-terminal variations in the protein sequences; 4, genes with amino acid variations in their core sequence. [ Excel file] (146 kb) Regions of genomic plasticity in the genome of 168. Regions predicted by MaGe are marked in brown when also containing genomic island signatures, and in blue otherwise. Predictions not seen using MaGe are marked in green. Phage regions are highlighted in yellow. The predicted genomic regions are marked with 'Y' when they have been described previously. [ Excel file] (73 kb) Correspondence analysis of the amino acid distribution in the proteome of 168. The table lists the proteins according to their belonging to the integral inner-membrane (IIMP) class or to the bulk protein class. A reliability factor tells whether ascribing a protein to class I or class II has a strong relevance or not. [ Excel file] (567 kb)

EXCEL

tRNAs series observed in the original sequence of 168. The upper part reports tRNA series found in rDNA cluster spacers, whereas the lower part shows those that are found elsewhere on the chromosome. Subseries that are shared by several clusters are indicated by coloured boxes. The triad specific to the triple cluster rDNA I, H and G is indicated in a red box. [ Excel file] (36 kb) Syntactic feature updates in the 168 new genome sequence. The table identifies (comparing with the previously available sequence and annotation of B. subtilis 168): 1, new genes; 2, sequence corrections which resulted in gene fusion or fission; 3, genes with N-terminal and C-terminal variations in the protein sequences; 4, genes with amino acid variations in their core sequence. [ Excel file] (146 kb) Regions of genomic plasticity in the genome of 168. Regions predicted by MaGe are marked in brown when also containing genomic island signatures, and in blue otherwise. Predictions not seen using MaGe are marked in green. Phage regions are highlighted in yellow. The predicted genomic regions are marked with 'Y' when they have been described previously. [ Excel file] (73 kb) Correspondence analysis of the amino acid distribution in the proteome of 168. The table lists the proteins according to their belonging to the integral inner-membrane (IIMP) class or to the bulk protein class. A reliability factor tells whether ascribing a protein to class I or class II has a strong relevance or not. [ Excel file] (567 kb)

EXCEL

tRNAs series observed in the original sequence of 168. The upper part reports tRNA series found in rDNA cluster spacers, whereas the lower part shows those that are found elsewhere on the chromosome. Subseries that are shared by several clusters are indicated by coloured boxes. The triad specific to the triple cluster rDNA I, H and G is indicated in a red box. [ Excel file] (36 kb) Syntactic feature updates in the 168 new genome sequence. The table identifies (comparing with the previously available sequence and annotation of B. subtilis 168): 1, new genes; 2, sequence corrections which resulted in gene fusion or fission; 3, genes with N-terminal and C-terminal variations in the protein sequences; 4, genes with amino acid variations in their core sequence. [ Excel file] (146 kb) Regions of genomic plasticity in the genome of 168. Regions predicted by MaGe are marked in brown when also containing genomic island signatures, and in blue otherwise. Predictions not seen using MaGe are marked in green. Phage regions are highlighted in yellow. The predicted genomic regions are marked with 'Y' when they have been described previously. [ Excel file] (73 kb) Correspondence analysis of the amino acid distribution in the proteome of 168. The table lists the proteins according to their belonging to the integral inner-membrane (IIMP) class or to the bulk protein class. A reliability factor tells whether ascribing a protein to class I or class II has a strong relevance or not. [ Excel file] (567 kb)

EXCEL
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