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Open AccessResearch article

The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571

Kyung-Bum Lee1,2* email, Philippe De Backer3,4* email, Toshihiro Aono1 email, Chi-Te Liu1 email, Shino Suzuki1 email, Tadahiro Suzuki1 email, Takakazu Kaneko5 email, Manabu Yamada5 email, Satoshi Tabata5 email, Doris M Kupfer6 email, Fares Z Najar6 email, Graham B Wiley6 email, Bruce Roe6 email, Tim T Binnewies7 email, David W Ussery7 email, Wim D'Haeze4 email, Jeroen Den Herder3,4 email, Dirk Gevers3,4,8 email, Danny Vereecke3,4 email, Marcelle Holsters3,4 email and Hiroshi Oyaizu1 email

1  Laboratory of Plant Biotechnology, Biotechnology Research Center, University of Tokyo, Tokyo 113-8657, Japan

2  Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima 411-8540, Japan

3  Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), 9052 Gent, Belgium

4  Department of Molecular Genetics, Ghent University, 9052 Gent, Belgium

5  Kazusa DNA Research Institute, Chiba 292-0818, Japan

6  Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019-3051, USA

7  Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark

8  Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA

author email corresponding author email* Contributed equally

BMC Genomics 2008, 9:271doi:10.1186/1471-2164-9-271

Published: 4 June 2008

Additional files

Additional file 1:

Overview of the genes, their properties, and translation products present in the genome of A. caulinodans. From left to right: unique ID for each A. caulinodans gene; indication of the gene function based on homology; functional classification of genes according to Riley [26]; GC content at the third position of codons in percent; GC content of a gene in percent; start/stop, position of start codon or stop codon of a gene on the plus or minus strand, respectively; stop/start, position of stop codon or start codon of a gene on the plus or minus strand, respectively; strand, coding sequence on the plus or minus strand; protein sequence.

Format: XLS Size: 2.4MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 2:

Overview of the properties of the 45 α-proteobacterial genomes of the data set. From left to right: bacterial strain; type of replicon; NCBI database identification code; size in Mbp; GC content of the replicon; number of proteins encoded by the replicon; number of structural RNA elements on the replicon.

Format: XLS Size: 163KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 3:

Whole genome comparison of A. caulinodans ORS571 and Xanthobacter autotrophicus Py2 using the ARTEMIS Comparison Tool [25]. Red and blue lines connect similar sequences and similar sequences that are inverted between strains, respectively.

Format: PDF Size: 2.4MB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 4:

Overview of genes present in the A. caulinodans ORS571 genome and absent in the Xanthobacter autotrophicus Py2 genome. From left to right: unique ID for each A. caulinodans gene; indication of the gene function based on homology; GC content at the third position of codons in percent; GC content of a gene in percent.

Format: XLS Size: 168KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 5:

Chemotaxis and motility genes in the A. caulinodans genome. From left to right: unique ID for each A. caulinodans gene; indication of the gene function based on homology; functional classification of genes according to Riley [26]; GC content at the silent third base of codons in percent; GC content of a gene in percent.

Format: XLS Size: 33KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 6:

Putative detoxification genes in A. caulinodans. From left to right: unique ID for each A. caulinodans gene; indication of the gene function based on homology; functional classification of genes according to Riley [26]; GC content at the third position of codons in percent; GC content of a gene in percent.

Format: XLS Size: 23KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 7:

Genes encoding surface-associated components in the A. caulinodans genome. From left to right: unique ID for each A. caulinodans gene; indication of the gene function based on homology; GC content at the third position of codons in percent; GC content of a gene in percent.

Format: XLS Size: 31KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 8:

Genes in the A. caulinodans genome dedicated to transport. From left to right: unique ID for each A. caulinodans gene; indication of the gene function based on homology; functional classification of genes according to Riley [26]; position of start codon or stop codon of a gene on the plus or minus strand, respectively; position of stop codon or start codon of a gene on the plus or minus strand, respectively; coding sequence on the plus or minus strand.

Format: XLS Size: 117KB Download file

This file can be viewed with: Microsoft Excel Viewer

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