Reconstructing histories of complex gene clusters on a phylogeny

Journal of Computational Biology

Volumn 17, Issue 9, 2010, Pages 1267-1279

  Vinař, Tomář ^a   Brejová, Broňa ^a   Song, Giltae ^b   Siepel, Adam ^c  

^a Physics and Informatics   (Slovakia)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

^c Plant Breeding and Genetics Section in the School of Integrative Plant Science   (United States)

Author keywords

computational molecular biology; evolution; gene finding; genomes; HMM

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; BIOLOGICAL MODEL; GENE DUPLICATION; GENOME; GENOMICS; HUMAN; METHODOLOGY; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PHYLOGENY; SPECIES DIFFERENTIATION;

ALGORITHMS; ANIMALS; BASE SEQUENCE; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENETIC SPECIATION; GENOME; GENOMICS; HUMANS; MODELS, GENETIC; MULTIGENE FAMILY; PHYLOGENY;

HUMAN IMMUNODEFICIENCY VIRUS;

EID: 77958059774     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2010.0090     Document Type: Article

References (34)

1. An, P., et al. 2004. APOBEC3G genetic variants and their influence on the progression to AIDS. J. Virol. 78, 11070-11076.
2. Becker, T. S., and Lenhard, B. 2007. The random versus fragile breakage models of chromosome evolution: a matter of resolution. Mol. Genet. Genom. 278, 487-491.
3. Benson, G., and Dong, L. 1999. Reconstructing the duplication history of a tandem repeat. Int. Conf. Intell. Syst. Mol. Biol. 44-53.
4. Bertrand, D., Lajoie, M., and El-Mabrouk, N. 2008. Inferring ancestral gene orders for a family of tandemly arrayed genes. J. Comput. Biol. 15, 1063-1067.
5. Birtle, Z., Goodstadt, L., and Ponting, C. 2005. Duplication and positive selection among hominin-specific PRAME genes. BMC Genom. 6, 120.
6. Bitti, P. P., et al. 2001. Association between the ancestral haplotype HLA A30B18DR3 and multiple sclerosis in central Sardinia. Genet. Epidemiol. 20, 271-273.
7. Degenhardt, J. D., et al. 2009. Copy number variation of CCL3-like genes affects rate of progression to simian-AIDS in Rhesus Macaques (Macaca mulatta). PLoS Genet. 5, e1000346.
8. Dumas, L., Kim, Y. H., Karimpour-Fard, A., et al. 2007. Gene copy number variation spanning 60 million years of human and primate evolution. Genome Res. 17, 1266-1267.
9. Edgar, R. C. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinform. 5, 113.
10. Elemento, O., Gascuel, O., and Lefranc, M. P. 2002. Reconstructing the duplication history of tandemly repeated genes. Mol. Biol. Evol. 19, 278-278.
11. Finckh, U., et al. 2000. Genetic association of a cystatin C gene polymorphism with late-onset Alzheimer disease. Arch. Neurol. 57, 1579-1583.
12. Fitch, W. M. 1977. Phylogenies constrained by the crossover process as illustrated by human hemoglobins and a thirteen-cycle, eleven-amino-acid repeat in human apolipoprotein A-I. Genetics 86, 623-624.
13. Gibbs, R., et al. 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316, 222-224.
14. Green, E. D. 2001. Strategies for the systematic sequencing of complex genomes. Nat. Rev. Genet. 2, 573-573.
15. Hajdinjak, T., and Zagradisnik, B. 2004. Prostate cancer and polymorphism D85Y in gene for dihydrotestosterone degrading enzyme UGT2B15: frequency of DD homozygotes increases with Gleason Score. Prostate 59, 436-439.
16. Hastings, W. K. 1970. Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57, 97-109.
17. Holmes, I., and Bruno, W. J. 2001. Evolutionary HMMs: a Bayesian approach to multiple alignment. Bioinformatics 17, 803-810.
18. Karolchik, D. et al. 2008. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res. 36, D773-D779.
19. Kosiol, C., Vinar, T., da Fonseca, R. R., et al. 2008. Patterns of positive selection in six mammalian genomes. PLoS Genet. 4, e1000144.
20. Lajoie, M., Bertrand, D., El-Mabrouk, N., et al. 2007. Duplication and inversion history of a tandemly repeated genes family. J. Comput. Biol. 14, 462-468.
21. Lander, E. S. et al. 2001. Initial sequencing and analysis of the human genome. Nature 409, 860-921.
22. Ma, J., Ratan, A., Raney, B. J., et al. 2008. The infinite sites model of genome evolution. Proc. Natl. Acad. Sci. USA 105, 14254-14261.
23. Nadeau, J. H., and Taylor, B. A. 1984. Lengths of chromosomal segments conserved since divergence of man and mouse. Proc. Natl. Acad. Sci. USA 81, 814-818.
24. Ohno, S. 1970. Evolution by Gene Dupplication. Springer, Berlin.
25. Peng, Q., Pevzner, P. A., and Tesler, G. 2006. The fragile breakage versus random breakage models of chromosome evolution. PLoS Comput. Biol. 2, e14.
26. Ronquist, F., and Huelsenbeck, J. P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574.
27. Schwartz, S., Kent, W. J., Smit, A., et al. 2003. Human-mouse alignments with BLASTZ. Genome Res. 13, 103-107.
28. Tang, K. S., Chiu, H. F., Chen, H. H., et al. 2005. Link between colorectal cancer and polymorphisms in the uridinediphosphoglucuronosyltransferase 1A7 and 1A1 genes. World J. Gastroenterol. 11, 3250-3254.
29. Tang, M., Waterman, M., and Yooseph, S. 2002. Zinc finger gene clusters and tandem gene duplication. J. Comput. Biol. 9, 429-436.
30. Wapinski, I., Pfeffer, A., Friedman, N., et al. 2007. Automatic genome-wide reconstruction of phylogenetic gene trees. Bioinformatics 23, i549-558.
31. Zhang, L., Ma, B., Wang, L., et al. 2003. Greedy method for inferring tandem duplication history. Bioinformatics 19, 1497-1504.
32. Zhang, Y., Song, G., Hsu, C.-H., et al. 2009. Simultaneous history reconstruction for complex gene clusters in multiple species. Pac. Symp. Biocomput. 14, 162-173.
33. Zhang, Y., Song, G., Vinar, T., et al. 2008. Reconstructing the evolutionary history of complex human gene clusters. RECOMB 2008 29-49.
34. Zody, M. C., et al. 2008. Evolutionary toggling of the MAPT 17q21.31 inversion region. Nat. Genet. 40, 1076-1083.