MBE Advance Access published online on March 16, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi134
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1 Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de València, Apartat 22085, 46071 Valencia, Spain
* To whom correspondence should be addressed. Genome rearrangements have been studied in 30
Accepted March 3, 2005
Research Article
Genome Rearrangement Distances and Gene Order Phylogeny in
-Proteobacteria
Francisco J. Silva, E-mail: francisco.silva{at}uv.es
Abstract 
-proteobacterial complete genomes by comparing the order of a reduced set of genes on the chromosome. This set included those genes fulfilling several characteristics, the main ones being that an ortholog was present in every genome and that none of them had been acquired by horizontal gene transfer. Genome rearrangement distances were estimated, based on either the number of breakpoints or the minimal number of inversions separating two genomes. Breakpoint and inversion distances were highly correlated, indicating that inversions were the main type of rearrangement event in -Proteobacteria. In general, the progressive increase in sequence-based distances between genome pairs was associated to the increase in their rearrangement-based distances, but with several groups of distances not following this pattern. Compared with free-living enteric bacteria, the lineages of Pasteurellaceae were evolving, on average, to relatively higher rates of between 2.02 and 1.64, while the endosymbiotic bacterial lineages of Buchnera aphidicola and Wigglesworthia glossinidia were evolving at moderately higher rates of 1.38 and 1.35, respectively. Because we know that the rearrangement rate in the B. aphidicola lineage was close to zero during the last 100-150 million years of evolution, we deduced that a much higher rate took place in the first period of lineage evolution after the divergence of the Escherichia coli lineage. On the other hand, the lineage of the endosymbiont Blochmannia floridanus did present an almost identical rate to free-living enteric bacteria, indicating that the increase in the genome rearrangement rate is not a general change associated with bacterial endosymbiosis. Phylogenetic reconstruction based on rearrangement distances showed a different topology from the one inferred by sequence information. This topology broke the proposed monophyly of the three endosymbiotic lineages and placed Bl. floridanus as a closer relative to Escherichia coli than Yersinia pestis. These results indicate that the phylogeny of these insect endosymbionts is still an open question that will require the development of specific phylogenetic methods to confirm whether the sisterhood of the three endosymbiotic lineages is real or a consequence of a long-branch attraction phenomenon.-Proteobacteria; endosymbiont; gene order phylogeny; Buchnera; Blochmannia; Wigglesworthia.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  L.-W. Jiang, K.-L. Lin, and C. L. Lu OGtree: a tool for creating genome trees of prokaryotes based on overlapping genes Nucleic Acids Res., July 1, 2008; 36(suppl_2): W475 - W480. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Valle, A. N. Mabbett, G. C. Ulett, A. Toledo-Arana, K. Wecker, M. Totsika, M. A. Schembri, J.-M. Ghigo, and C. Beloin UpaG, a New Member of the Trimeric Autotransporter Family of Adhesins in Uropathogenic Escherichia coli J. Bacteriol., June 15, 2008; 190(12): 4147 - 4161. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Gomez-Valero, E. P.C. Rocha, A. Latorre, and F. J. Silva Reconstructing the ancestor of Mycobacterium leprae: The dynamics of gene loss and genome reduction Genome Res., August 1, 2007; 17(8): 1178 - 1185. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Homma, S. Fukuchi, Y. Nakamura, T. Gojobori, and K. Nishikawa Gene Cluster Analysis Method Identifies Horizontally Transferred Genes with High Reliability and Indicates that They Provide the Main Mechanism of Operon Gain in 8 Species of {gamma}-Proteobacteria Mol. Biol. Evol., March 1, 2007; 24(3): 805 - 813. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Madrid, J. Garcia, M. Pons, and A. Juarez Molecular Evolution of the H-NS Protein: Interaction with Hha-Like Proteins Is Restricted to Enterobacteriaceae J. Bacteriol., January 1, 2007; 189(1): 265 - 268. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. D. S. Cameron and R. J. Redfield Non-canonical CRP sites control competence regulons in Escherichia coli and many other {gamma}-proteobacteria Nucleic Acids Res., November 6, 2006; 34(20): 6001 - 6014. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. J. Silva, E. Belda, and S. E. Talens Differential annotation of tRNA genes with anticodon CAT in bacterial genomes Nucleic Acids Res., November 6, 2006; 34(20): 6015 - 6022. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. C. Lin, C. L. Lu, Y.-C. Liu, and C. Y. Tang SPRING: a tool for the analysis of genome rearrangement using reversals and block-interchanges. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W696 - W699. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Toft and M. A. Fares GRAST: a new way of genome reduction analysis using comparative genomics Bioinformatics, July 1, 2006; 22(13): 1551 - 1561. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. M. Fraser-Liggett Insights on biology and evolution from microbial genome sequencing Genome Res., December 1, 2005; 15(12): 1603 - 1610. [Abstract] [Full Text] [PDF]
|
|