SpringerProtocols: Abstract: Analyzing Patterns of Microbial Evolution Using the Mauve Genome Alignment System

Analyzing Patterns of Microbial Evolution Using the Mauve Genome Alignment System

By: Aaron E Darling², Todd J Treangen³, Xavier Messeguer⁴, Nicole T Perna⁵

Abstract

Full Text

Download PDF (1128K)

During the course of evolution, genomes can undergo large-scale mutation events such as rearrangement and lateral transfer. Such mutations can result in significant variations in gene order and gene content among otherwise closely related organisms. The Mauve genome alignment system can successfully identify such rearrangement and lateral transfer events in comparisons of multiple microbial genomes even under high levels of recombination. This chapter outlines the main features of Mauve and provides examples that describe how to use Mauve to conduct a rigorous multiple genome comparison and study evolutionary patterns.

Affiliation(s): (2) Department of Computer Scienc, University of Wisconsin-Madison, Madison, WI 53706
(3) Department of Software, Technical University of Catalonia-Barcelona, Barcelona
(4) Department of Software, Technical University of Catalonia-Barcelona, Barcelona Supercomputing Center (BSC), Barcelona
(5) Department of Animal Health and Biomedical Sciences Genome Center, University of Wisconsin-Madison, Barcelona

Book Title: Comparative Genomics

Series: Methods in Molecular Biology | Volume: 396 | Pub. Date: Nov-29-2007 | Page Range: 135-152 | DOI: 10.1007/978-1-59745-515-2_10

Subject: Genetics/Genomics

Key Words: Microbial evolution - sequence alignment - comparative genomics - genome alignment - genome rearrangement - lateral transfer - Yersinia pestis

References

Download References

1.	Needleman, S. B. and Wunsch, C. D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443–453.

2.	Smith, T. F. and Waterman, M. S. (1981) Identification of common molecular subsequences. J. Mol. Biol. 147, 195–197.

3.	Higgins, D. G. and Sharp, P. M. (1988) CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73, 237–244.

4.	Notredame, C., Higgins, D. G., and Heringa, J. (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205–217.

5.	Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797.

6.	Lee, C., Grasso, C., and Sharlow, M. F. (2002) Multiple sequence alignment using partial order graphs. Bioinformatics 18, 452–464.

7.	Abouelhoda, M. I. and Ohlebusch, E. (2003) A local chaining algorithm and its applications in comparative genomics. Algorithms in Bioinformatics, Proceedings 2812, 1–16.

8.	Haas, B. J., Delcher, A. L., Wortman, J. R., and Salzberg, S. L. (2004) DAGchainer: a tool for mining segmental genome duplications and synteny. Bioinformatics 20, 3643–3646.

9.	Hampson, S. E., Gaut, B. S., and Baldi, P. (2005) Statistical detection of chromosomal homology using shared-gene density alone. Bioinformatics 21, 1339–1348.

10.	Hampson, S., McLysaght, A., Gaut, B., and Baldi, P. (2003) LineUp: statistical detection of chromosomal homology with application to plant comparative genomics. Genome Res. 13, 999–1010.

11.	Tesler, G. (2002) GRIMM: genome rearrangements web server. Bioinformatics 18, 492–493.

12.	Spang, R., Rehmsmeier, M., and Stoye, J. (2002) A novel approach to remote homology detection: Jumping alignments. Journal of Computational Biology 9, 747–760.

13.	Calabrese, P. P., Chakravarty, S., and Vision, T. J. (2003) Fast identification and statistical evaluation of segmental homologies in comparative maps. Bioinformatics 19, i74–i80.

14.	Darling, A. E., Mau, B., Blattner, F. R., and Perna, N. T. (2004) GRIL: genome rearrangement and inversion locator. Bioinformatics 20, 122–124.

15.	Durbin, R. (1998) Biological Sequence Analysis: Probabalistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, UK, pp. xi, 356.

16.	Fitch, W. M. (2000) Homology a personal view on some of the problems. Trends Genet. 16, 227–231.

17.	Larget, B., Kadane, J. B., and Simon, D. L. (2005) A Bayesian approach to the estimation of ancestral genome arrangements. Mol. Phylogenet. Evol. 36, 214–223.

18.	Bourque, G. and Pevzner, P. A. (2002) Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res. 12, 26–36.

19.	Wu, S. and Gu, X. (2003) Algorithms for multiple genome rearrangement by signed reversals. Pac. Symp. Biocomput. 363–374.

20.	Lu, C. L., Wang, T. C., Lin, Y. C., and Tang, C. Y. (2005) ROBIN: a tool for genome rearrangement of block-interchanges. Bioinformatics 21, 2780–2782.

21.	Yancopoulos, S., Attie, O., and Friedberg, R. (2005) Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21, 3340–3346.

22.	Holder, M. and Lewis, P. O. (2003) Phylogeny estimation: traditional and Bayesian approaches. Nat. Rev. Genet. 4, 275–284.

23.	Yang, Z., Ro, S., and Rannala, B. (2003) Likelihood models of somatic mutation and codon substitution in cancer genes. Genetics 165, 695–705.

24.	Lunter, G., Ponting, C. P., and Hein, J. (2006) Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model. PLoS Comput. Biol. 2, e5.

25.	Darling, A. C., Mau, B., Blattner, F. R., and Perna, N. T. (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14, 1394–1403.

26.	Brudno, M., Malde, S., Poliakov, A., et al. (2003) Glocal alignment: finding rearrangements during alignment. Bioinformatics 19, i54–i62.

27.	Ovcharenko, I., Loots, G. G., Giardine, B. M., et al. (2005) Mulan: multiple-sequence local alignment and visualization for studying function and evolution. Genome Res. 15, 184–194.

28.	Treangen, T. J. and Messeguer, X. (2006) M-GCAT: interactively and efficiency constructing large-scale multiple genome comparision frameworks in closely related species. BMC Bioinformatics 7, 433.

29.	Kurtz, S., Phillippy, A., Delcher, A. L., et al. (2004) Versatile and open software for comparing large genomes. Genome Biol. 5, R12.

30.	Hohl, M., Kurtz, S., and Ohlebusch, E. (2002) Efficient multiple genome alignment. Bioinformatics 18, S312–S320.

31.	Blanchette, M., Kent, W. J., Riemer, C., et al. (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14, 708–715.

32.	Bray, N. and Pachter, L. (2004) MAVID: constrained ancestral alignment of multiple sequences. Genome Res. 14, 693–699.

33.	Brudno, M., Do, C. B., Cooper, G. M., et al. (2003) LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13, 721–731.

34.	Choi, K. P., Zeng, F., and Zhang, L. (2004) Good spaced seeds for homology search. Bioinformatics 20, 1053–1059.

35.	Henz, S. R., Huson, D. H., Auch, A. F., Nieselt-Struwe, K., and Schuster, S. C. (2005) Whole-genome prokaryotic phylogeny. Bioinformatics 21, 2329–2335.

36.	Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425.

37.	Cleri, D. J., Vernaleo, J. R., Lombardi, L. J., et al. (1997) Plague pneumonia disease caused by Yersinia pestis. Semin. Respir. Infect. 12, 12–23.

38.	Carniel, E. (2003) Evolution of pathogenic Yersinia, some lights in the dark. Adv. Exp. Med. Biol. 529, 3–12.

39.	Chain, P. S., Carniel, E., Larimer, F. W., et al. (2004) Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc. Natl. Acad. Sci. USA 101, 13,826–13,831.

40.	Hinnebusch, B. J. (2005) The evolution of flea-borne transmission in Yersinia pestis. Curr. Issues Mol. Biol. 7, 197–212.

41.	Perna, N. T., Plunkett, G., 3rd, Burland, V., et al. (2001) Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409, 529–533.

42.	Hsiao, W. W., Ung, K., Aeschliman, D., Bryan, J., Finlay, B. B., and Brinkman, F. S. (2005) Evidence of a large novel gene pool associated with prokaryotic genomic islands. PLoS Genet. 1, e62.

43.	Tettelin, H., Masignani, V., Cieslewicz, M. J., et al. (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc. Natl. Acad. Sci. USA 102, 13,950–13,955.

44.	Terzian, C., Ferraz, C., Demaille, J., and Bucheton, A. 2000) Evolution of the Gypsy endogenous retrovirus in the Drosophila melanogaster subgroup. Mol. Biol. Evol. 17, 908–914.

45.	Lord, P. W., Selley, J. N., and Attwood, T. K. (2002) CINEMA-MX: a modular multiple alignment editor. Bioinformatics 18, 1402–1403.

Comments (Loading...)

Post comment/View all comments