Abstract
Given the mitochondrial gene orders and the phylogenetic relationship of a set of unichromosomal taxa, we study the problem of finding a plausible and parsimonious assignment of genomic rearrangement events to the edges of the given phylogenetic tree. An algorithm called algorithm TreeREx (tree rearrangement explorer) is proposed for solving this problem heuristically. TreeREx is based on an extended version of algorithm CREx (common interval rearrangement explorer, [4]) that heuristically computes pairwise rearrangement scenarios for gene order data. As phylogenetic events in such scenarios reversals, transpositions, reverse transpositions, and tandem duplication random loss (TDRL) operations are considered. CREx can detect such events as patterns in the signed strong interval tree, a data structure representing gene groups that appear consecutively in a set of two gene orders. TreeREx then tries to assign events to the edges of the phylogenetic tree, such that the pairwise scenarios are reflected on the paths of the tree. It is shown that TreeREx can automatically infer the events and the ancestral gene orders for realistic biological examples of mitochondrial gene orders. In an analysis of gene order data for teleosts, algorithm TreeREx is able to identify a yet undocumented TDRL towards species Bregmaceros nectabanus.
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References
Arndt, A., Smith, M.J.: Mitochondrial gene rearrangement in the sea cucumber genus cucumaria. Mol. Biol. Evol. 15(8), 9–16 (1998)
Bérard, S., Bergeron, A., Chauve, C., Paul, C.: Perfect sorting by reversals is not always difficult. IEEE/ACM Transaction on Computational Biology and Bioinformatics 4(1), 4–16 (2007)
Bergeron, A., Chauve, C., de Montgolfier, F., Raffinot, M.: Computing common intervals of k permutations, with applications to modular decomposition of graphs. In: Brodal, G.S., Leonardi, S. (eds.) ESA 2005. LNCS, vol. 3669, pp. 779–790. Springer, Heidelberg (2005)
Bernt, M., Merkle, D., Ramsch, K., Fritzsch, G., Perseke, M., Bernhard, D., Schlegel, M., Stadler, P.F., Middendorf, M.: Crex: inferring genomic rearrangements based on common intervals. Bioinformatics 23, 2957–2958 (2007)
Blanchette, M., Kunisawa, T., Sankoff, D.: Gene order breakpoint evidence in animal mitochondrial phylogeny. J. Mol. Evol. 49, 193–203 (1999)
Boore, J.L.: Mitochondrial gene arrangement database (2006), http://evogen.jgi.doe.gov/
Booth, K.S., Lueker, G.S.: Testing for the consecutive ones property, interval graphs, and graph planarity using pq-tree algorithms. Journal of Computer and System Sciences 13, 335–379 (1976)
Caprara, A.: The reversal median problem. INFORMS Journal on Computing 15, 93–113 (2003)
Chaudhuri, K., Chen, K., Mihaescu, R., Rao, S.: On the tandem duplication-random loss model of genome rearrangement. In: SODA, pp. 564–570 (2006)
Heber, S., Stoye, J.: Algorithms for finding gene clusters. In: Gascuel, O., Moret, B.M.E. (eds.) WABI 2001. LNCS, vol. 2149, pp. 252–263. Springer, Heidelberg (2001)
Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M.: Evolution of the deep-sea gulper eel mitochondrial genomes: large-scale gene rearrangements originated within the eels. Mol. Biol. Evol. 20, 1917–1924 (2003)
Lavrov, D.V., Boore, J.L., Brown, W.M.: Complete mtdna sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: duplication and nonrandom loss. Mol. Biol. Evol. 19, 163–169 (2002)
Littlewood, D.T.J., Smith, A.B., Cloug, h.K.A., Emson, R.H.: The interrelationships of the echinoderm classes: morphological and molecular evidence. Biol. J. Linn. Soc. 61, 409–438 (1997)
Miya, M., Takeshima, H., Endo, H., Ishiguro, N.B., Inous, J.G., Mukai, T., Satoh, T.P., Yamagucki, M., Kawaguchi, A., Mabuchi, K., Shirai, S.M., Nishida, M.: Major patterns of higher teleost phylogenies: a new perspective based on 100 complete mitochondrial dna sequences. Mol. Phyl. Evol. 26, 121–138 (2003)
Mooi, R., David, B.: Skeletal homologies of echinoderms. Paleont. Soc. Papers 3, 305–335 (1997)
Parida, L.: Using pq structures for genomic rearrangement phylogeny. Journal of Computational Biology 13(10), 1685–1700 (2006)
Perseke, M., Fritzsch, G., Ramsch, K., Bernt, M., Merkle, D., Middendorf, M., Bernhard, D., Stadler, P.F., Schlegel, M.: Evolution of mitochondrial gene orders in echinoderms. Mol. Phyl. Evol. (in press, 2008)
Sankoff, D.: Analytical approaches to genomic evolution. Biochimie 75, 409–413 (1993)
Scouras, A., Beckenbach, K., Arndt, A., Smith, M.J.: Complete mitochondrial genome dna sequence for two ophiuroids and a holothuroid: the utility of protein gene sequence and gene maps in the analyses of deep deuterostome phylogeny. Mol. Phyl. Evol. 31(1), 50–65 (2004)
Uno, T., Yagiura, M.: Fast algorithms to enumerate all common intervals of two permutations. Algorithmica 26(2), 290–309 (2000)
Zhao, H., Bourque, G.: Recovering true rearrangement events on phylogenetic trees. In: Tesler, G., Durand, D. (eds.) RECMOB-CG 2007. LNCS (LNBI), vol. 4751, pp. 149–161. Springer, Heidelberg (2007)
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Bernt, M., Merkle, D., Middendorf, M. (2008). An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree. In: Nelson, C.E., Vialette, S. (eds) Comparative Genomics. RECOMB-CG 2008. Lecture Notes in Computer Science(), vol 5267. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-87989-3_11
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DOI: https://doi.org/10.1007/978-3-540-87989-3_11
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