Abstract
Deriving phylogeny of rapidly evolving viral genomes is one of the most challenging problems in evolutionary studies since gene-based phylogenies often produce conflicting evolutionary trees. Phylogenetic reconstruction methods that consider whole genomes are becoming more reliable with the increasing availability of complete genome sequences and the development of algorithms to compare entire genomes. Here we employ a gene rearrangement-based approach to study Baculovirus phylogeny. Since genome rearrangement algorithms require the set of genes shared between all genomes, the most challenging problem in analyzing rapidly evolving genomes is generating this set of genes. Indeed, there are fewer and fewer genes shared between N species as N increases. We address this challenge by iteratively considering smaller sets of related genomes to find conserved genes. Baculovirus was chosen as a test case because a large number of its constituent genomes have been sequenced and its evolutionary relationships are well studied. The resulting phylogenies show clear separation of Baculoviridae into Nucleopolyhedrovirus (NPV) and Granulovirus (GV) as well as the separation of NPVs into groups I and II. Further species separation results in phylogenetic relationships that are largely consistent with conventional gene-based approaches, with some differences that provide insight into the rearrangements of Baculoviridae genomes. Our open source software, MULGOR (MULtiple Genome Order), which analyzes genes shared between multiple small rapidly evolving genomes, is available at http://realm.sdsc.edu/MULGOR/.
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References
Albrecht, J., Nicholas, J., Biller, D., Cameron, K.R., Biesinger, B., Newman, C., Wittmann, S., Craxton, M.A., Coleman, H., Fleckenstein, B., Honess, R.W.: Primary structure of the herpesvirus saimiri genome. J. Virol. 66, 5047–5058 (1992)
Belda, E., Moya, A., Silva, F.: Genome Rearrangement Distances and Gene Order Phylogeny in γ-Proteobacteria. Molecular Biology and Evolution. 22, 1456–1467 (2005)
Blanchette, M., Bourque, G., Sankoff, D.: Breakpoint phylogenies. In: Miyano, S., Takagi, T. (eds.) Genome Informatics 1997, pp. 25–34. Univ. Academy Press (1997)
Bourque, G., Pevzner, P.: Genome-Scale Evolution: Reconstructing Gene Orders in the Ancestral Species. Genome Research. 12(1), 26–36 (2002)
Bourque, G., Pevzner, P.A., Tesler, G.: Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. Genome Research. 14, 507–516 (2004)
Bryant, D.: The complexity of calculating exemplar distances. In: Sankoff, D., Nadeau, J. (eds.) Comparative Genomics, pp. 207–212. Kluwer Academic Publishers, Dordrecht (2000)
Cormen, T.H., Leiserson, C.E., Riverst, R.L, Stein, C.: Introduction to Algorithms. Mc-Graw Hill, New York (2001)
El-Mabrouk, N.: Genome rearrangement by reversals and insertions/deletions of contiguous segments. In: Giancarlo, R., Sankoff, D. (eds.) CPM 2000. LNCS, vol. 1848, pp. 222–234. Springer, Heidelberg (2000)
Hannenhalli, S., Pevzner, P.: Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). In: Theory of Computing STOC 95, pp. 178–189. ACM Press, New York (1995)
Hannenhalli, S., Chappey, C., Koonin, E., Pevzner, P.: Genome Sequence Comparison and Scenarios for Gene Rearrangements: A Test Case. Genomics. 30, 299–311 (1995)
Hanson, L., Rudis, M., Vasquez-Lee, M., Montgomery, D.: A broadly applicable method to characterize large DNA viruses and adenoviruses based on the DNA polymerase gene. Virology Journal 3, 28 (2006)
Herniou, E., Luque, T., Chen, X., Vlak, J., Winstanley, D., Cory, D., O’Reilly, D.: Use of Whole Genome Sequence Data To Infer Baculovirus Phylogeny. Journal of Virology 75(17), 8117–8126 (2001)
Herniou, E., lszewski, O., Cory, J., O’Reilly, D.: The Genome Sequence and Evolution of Baculoviruses. Annual Review of Entomology 48, 211–234 (2003)
Herniou, E., Olszewski, J., O’Reilly, D., Cory, J.: Ancient Coevolution of Baculoviruses and Their Insect Hosts. Journal of Virology. 78(7), 3244–3251 (2004)
Graur, D., Li, W.: Fundamentals of Molecular Evolution. In: Sinauer Associates, Sunderland, Massachusetts (2000)
Koonin, E.V., Aravind, L., Kondrashov, A.S.: The impact of comparative genomics on our understanding of evolution. Cell 101(6), 573–576 (2000)
Li, L., Stoeckert, C.J., Roos, D.S.: OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes. Genome Res. 13(9), 2178–2189 (2003)
Moret, B.M.E., Siepel, A.C., Tang, J., Liu, T.: Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data. In: Guigó, R., Gusfield, D. (eds.) WABI 2002. LNCS, vol. 2452, pp. 521–536. Springer, Heidelberg (2002)
Murphy, W.J., Larkin, D.M., van der Wind, A.E., Bourque, G., Tesler, G., Auvil, L., Beever, J.E., Chowdhary, B.P., Galibert, F., Gatzke, L., Hitte, C., Meyers, S.N., Milan, D., Ostrander, E.A., Pape, G., Parker, H.G., Raudsepp, T., Rogatcheva, M.B., Schook, L.B., Skow, L.C., Welge, M., Womack, J.E., O’brien, S.J., Pevzner, P.A., Lewin, H.A.: Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309(5734), 613–617 (2005)
Murphy, W., Pevzner, P., O’Brien, S.: Mammalian phylogenomics comes of age. Trends in Genetics. 20(12), 631–639 (2004)
Olmstead, R., Palmer, J.: Chloroplast DNA systematics: a review of methods and data analysis. Amer. J. Bot. 81, 1205–1224 (1994)
Palmer, J., Herbon, L.: Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence. J. Mol. Evol. 27, 87–97 (1988)
Remm, D., Storm, C.E.V., Sonnhammer, E.L.L.: Automatic Clustering of Orthologs and In-paralogs from Pairwise Species Comparisons. J. Mol. Biol. 314, 1041–1052
Rokas, A., Holland, P.W.H.: Rare genomic changes as a tool for phylogenetics. Trends in Ecology & Evolution 15(11), 454–459 (2000)
Sankoff, D.: Genome rearrangement with gene families. Technical Report, Centre de recherches mathématiques, Université de Montréal (1999)
Sankoff, D., Blanchette, M.: Multiple genome rearrangement and breakpoint phylogeny. Journal of Computational Biology 5, 555–570 (1998)
Snel, B., Bork, P., Huynen, M.: Genome phylogeny based on gene content. Nature Genetics. 21, 108–110 (1999)
Snel, B., Bork, P., Huynen, M.: Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene Content. Nature. 417, 399–403 (2002)
Tesler, G., Pavel, P.: Genome Rearrangements in Mammalian Evolution: Lessons From Human and Mouse Genomes. Genome Res. 13, 37–45 (2003)
Thornton, J.W., DeSalle, R.: Gene family evolution and homology: genomics meets phylogenetics. Annu. Rev. Genomics Hum. Genet. 1, 41–73 (2000)
Wang, L., Warnow, T.: Estimating true evolutionary distances between genomes. In: Proceedings of the Thirty-third Symposium on Theory of Computing (STOC’01), pp. 637–646. ACM Press, New York (2001)
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Goodman, D., Ollikainen, N., Sholley, C. (2007). Baculovirus Phylogeny Based on Genome Rearrangements. In: Tesler, G., Durand, D. (eds) Comparative Genomics. RECOMB-CG 2007. Lecture Notes in Computer Science(), vol 4751. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74960-8_6
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DOI: https://doi.org/10.1007/978-3-540-74960-8_6
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