Research article
Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments
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* Corresponding author: Eshel Ben-Jacob eshelbj@gmail.com
- † Equal contributors
1 The Sackler School of Physics and Astronomy, Tel Aviv University, P.O. Box 39040, Tel Aviv 69978, Israel
2 The Sackler School of Medicine, Tel Aviv University, P.O. Box 39040, Tel Aviv 69978, Israel
3 Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
4 Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
5 Laboratory of Microbiology, Wageningen University, Wageningen 6703 HB, Netherlands
6 Laboratory of System Biology and Analysis of High-throughput data, Institute of Evolution, University of Haifa, Haifa 31905, Israel
7 Department of Biological Services, Weizmann Institute of Science, Rehovot 76100, Israel
8 Department of Mathematical Analysis, Faculty of Mechanics and Mathematics, Moscow State University, Moscow 119991, Russia
9 A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119991, Russia
10 Genotypic Technology (P) Ltd, Bangalore 560094, India
11 Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
12 The Center for Theoretical and Biological Physics, University of California San Diego, La Jolla, California 92093, USA
BMC Genomics 2010, 11:710 doi:10.1186/1471-2164-11-710
Published: 17 December 2010Additional files
Additional file 1:
Detailed supplementary information. This file includes additional information on P. vortex physiology, comparison of sequencing methods, validation of P. vortex annotation and materials and methods.
Format: PDF Size: 1.8MB Download file
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Additional file 2:
Movement of a single vortex, 500× magnification and twice the real speed.
Format: WMV Size: 958KB Download file
Additional file 3:
Early stage of colony organization including the formation of vortices and moving groups of bacteria. The magnification is 50× magnification and 60× rate.
Format: WMV Size: 405KB Download file
Additional file 4:
Dynamic imaging of swarming by light microscopy. Single branch of a swarming culture moving on MH (1.5% w/v) agar is presented. Magnification 400× and 4 times the actual speed.
Format: WMV Size: 3.4MB Download file
Additional file 5:
Effect of extracellular material derived from plates containing swarming cells on P. vortex swarming. Light microscopy of P. vortex moving on MH agar (0.3% w/v), extending into an area where extracellular material derived from washes of swarming cells was delivered by toothpick and allowed to soak into the agar. (A) Cell mass starts to disperse as it approaches the area of the extract. (B) Cell mass has dispersed into area of extract.
Format: WMV Size: 787KB Download file
Additional file 6:
Effect of number of extracellular materials derived from plates containing swarming cells on P. vortex swarming. Light microscopy of P. vortex moving on MH agar (0.3% w/v), extending into an area where extracellular material derived from washes of swarming cells. (A) Cell mass is evaluating the gradient and starts move towards the area with the extract. (B) Cell mass starts to disperse as it approaches the area of the extract. (C) Additional cells are moving into this area from further back in the colony.
Format: WMV Size: 1.2MB Download file
Additional file 7:
A set of 500 complete bacterial genomes of 2-10 Mbp genome size, which were used in the detailed comparative genomic analysis with the P. vortex genome.
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Additional file 8:
A subset of 50 soil bacterial genomes with genome size 4-8 Mbp (closer to the P. vortex genome size), that were used in the comparative genome analysis.
Format: XLS Size: 28KB Download file
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Additional file 9:
List of 153 sporulation genes encoded by the P. vortex genome that are responsible for cell division, engulfment, cortex and coat synthesis, maturation and germination processes.
Format: XLS Size: 42KB Download file
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Additional file 10:
List of conserved PFAM domains, TIGR domains, COG categories or KEGG pathways associated with sporulation that were used in identification of sporularion genes in P. vortex.
Format: XLS Size: 19KB Download file
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Additional file 11:
A compiled list of Pfam domains that was used to identify Two-Component System genes is presented.
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Additional file 12:
A compiled list of Pfam domains that was used to identify Transcription Factor genes is presented.
Format: XLS Size: 23KB Download file
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Additional file 13:
A compiled list of COG categories that was used to identify transport related genes is presented.
Format: XLS Size: 30KB Download file
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Additional file 14:
A compiled list of COG categories that was used to identify defense related genes is presented.
Format: XLS Size: 16KB Download file
This file can be viewed with: Microsoft Excel Viewer