Abstract
We study the problem of phylogenetic reconstruction based on gene order for whole genomes. We define three genomic distances between whole genomes represented by signed sequences, based on the matching of similar segments of genes and on the notions of breakpoints, conserved intervals and common intervals. We use these distances and distance based phylogenetic reconstruction methods to compute a phylogeny for a group of 12 complete genomes of γ-Proteobacteria.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Altschul, S.F., Maden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res. 25(17), 3389–3402 (1997)
Belda, E., Moya, A., Silva, F.J.: Genome rearrangement distances and gene order phylogeny in γ-proteobacteria. Mol. Biol. Evol. 22(6), 1456–1467 (2005)
Bérard, S., Bergeron, A., Chauve, C.: Conserved structures in evolution scenarios. In: Lagergren, J. (ed.) RECOMB-WS 2004. LNCS (LNBI), vol. 3388, pp. 1–15. Springer, Heidelberg (2005)
Bergeron, A., Stoye, J.: On the similarity of sets of permutations and its applications to genome comparison. In: Warnow, T.J., Zhu, B. (eds.) COCOON 2003. LNCS, vol. 2697, pp. 68–79. Springer, Heidelberg (2003)
Blanchette, M., Kunisawa, T., Sankoff, D.: Gene order breakpoint evidence in animal mitochondrial phylogeny. J. Mol. Evol. 49(2), 193–203 (1999)
Blin, G., Chauve, C., Fertin, G.: The breakpoints distance for signed sequences. In: 1st International Conference on Algorithms and Computational Methods for Biochemical and Evolutionary Networks, CompBioNets 2004. Texts in Algorithms, vol. 3, pp. 3–16. KCL Publications (2004)
Blin, G., Rizzi, R.: Conserved interval distance computation between non-trivial genomes. In: Wang, L. (ed.) COCOON 2005. LNCS, vol. 3595, pp. 22–31. Springer, Heidelberg (2005) (to appear)
Bourque, G., Pevzner, P.A., Tesler, G.: Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse and rat genomes. Genome Res. 14(4), 507–516 (2004)
Bourque, G., Zdobnov, E.M., Bork, P., Pevzner, P.A., Tesler, G.: Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res. 15(1), 98–110 (2005)
Chen, X., Zheng, J., Fu, Z., Nan, P., Zhong, Y., Lonardi, S., Jiang, T.: Computing the assignment of orthologous genes via genome rearrangement. In: 3rd Asia-Pacific Bioinformatics Conference 2005, pp. 363–378. Imperial College Press (2005)
Earnest-DeYoung, J.V., Lerat, E., Moret, B.M.E.: Reversing gene erosion: Reconstructing ancestral bacterial genomes from gene-content and order data. In: Jonassen, I., Kim, J. (eds.) WABI 2004. LNCS (LNBI), vol. 3240, pp. 1–13. Springer, Heidelberg (2004)
Gascuel, O. (ed.): Mathematics of Evolution and Phylogeny. Oxford University Press, Oxford (2005)
Herbeck, J.T., Degnan, P.H., Wernegreen, J.J.: Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (γ-proteobacteria). Mol. Biol. Evol. 22(3), 520–532 (2004)
Lefebvre, J.-F., El-Mabrouk, N., Tillier, E., Sankoff, D.: Detection and validation of single gene inversions. Bioinformatics 19(suppl. 1), i190–i196 (2003)
Lerat, E., Daubin, V., Moran, N.A.: From gene tree to organismal phylogeny in prokaryotes: the case of γ-proteobacteria. PLoS Biology 1(1), 101–109 (2003)
Sankoff, D.: Genome rearrangement with gene families. Bioinformatics 15(11), 909–917 (1999)
Sankoff, D.: Short inversions and conserved gene clusters. Bioinformatics 18(10), 1305–1308 (2002)
Sankoff, D., Lefebvre, J.-F., Tillier, E., Maler, A., El-Mabrouk, N.: The distribution of inversion lengths in prokaryotes. In: Lagergren, J. (ed.) RECOMB-WS 2004. LNCS (LNBI), vol. 3388, pp. 97–108. Springer, Heidelberg (2005)
Swenson, K.M., Marron, M., Earnest-DeYoung, J.V., Moret, B.M.E.: Approximating the true evolutionary distance between two genomes. In: Proceedings of the seventh Workshop on Algorithms Engineering and Experiments and Second Workshop on Analytic Algorithmics and Combinatorics (ALENEX/ANALCO 2005), SIAM, Philadelphia (2005)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Blin, G., Chauve, C., Fertin, G. (2005). Genes Order and Phylogenetic Reconstruction: Application to γ-Proteobacteria. In: McLysaght, A., Huson, D.H. (eds) Comparative Genomics. RCG 2005. Lecture Notes in Computer Science(), vol 3678. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11554714_2
Download citation
DOI: https://doi.org/10.1007/11554714_2
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-28932-6
Online ISBN: 978-3-540-31814-9
eBook Packages: Computer ScienceComputer Science (R0)