Revealing mammalian evolutionary relationships by comparative analysis of gene clusters

Genome Biology and Evolution

Volumn 4, Issue 4, 2012, Pages 586-601

  Song, Giltae ^a   Riemer, Cathy ^a   Dickins, Benjamin ^a   Kim, Hie Lim ^a   Zhang, Louxin ^b   Zhang, Yu ^a   Hsu, Chih Hao ^c   Hardison, Ross C ^a   Green, Eric D ^d   Miller, Webb ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

^d NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

Author keywords

Conversion; Evolutionary inference; Gene clusters; KIR; Orthology

Indexed keywords

MAMMALIA;

PROTEIN;

ANIMAL; ARTICLE; CLASSIFICATION; COMPARATIVE STUDY; GENE CONVERSION; GENE DUPLICATION; GENETICS; GENOME; HUMAN; MAMMAL; MOLECULAR EVOLUTION; MULTIGENE FAMILY; PHYLOGENY;

ANIMALS; EVOLUTION, MOLECULAR; GENE CONVERSION; GENE DUPLICATION; GENOME; HUMANS; MAMMALS; MULTIGENE FAMILY; PHYLOGENY; PROTEINS;

EID: 84864077221     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evs032     Document Type: Conference Paper

References (79)

1. Abi-Rached L, Moesta A, Rajalingam R, Guethlein L, Parham P. 2010. Human-specific evolution and adaptation led to major qualitative differences in the variable receptors of human and chimpanzee natural killer cells. PLoS Genet. 6(11):e1001192.
2. Akahoshi M, et al. 2004. Association between IFNA genotype and the risk of sarcoidosis. Hum Genet. 114(5):503-509. (Pubitemid 38678930)
3. Bailey J, et al. 2002. Recent segmental duplications in the human genome. Science 297:1003-1007. (Pubitemid 34856032)
4. Birney E, Clamp M, Durbin R. 2004. GeneWise and Genomewise. Genome Res. 14:988-995. (Pubitemid 38660520)
5. Cadavid L, Lun C. 2009. Lineage-specific diversification of killer cell Iglike receptors in the owl monkey, a New World primate. Immunogenetics 61(1):27-41.
6. Chen J, Cooper D, Chuzhanova N, Ferec C, Patrinos G. 2007. Gene conversion: mechanisms, evolution and human disease. Nat Rev Genet. 8:762-775. (Pubitemid 47429210)
7. Chiu J, et al. 2006. OrthologID: automation of genome-scale ortholog identification within a parsimony framework. Bioinformatics 22:699-707.
8. Colobran R, et al. 2005. Multiple products derived from two CCL4 loci: high incidence of a new polymorphism in HIV+ patients. J Immunol. 174(9):5655-5664. (Pubitemid 40593207)
9. Datta R, Meacham C, Samad B, Neyer C, Sjlander K. 2009. Berkeley PHOG: phyloFacts orthology group prediction web server. Nucleic Acids Res. 37:W84-W89.
10. Degenhardt J, 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.
11. Dewey C. 2011. Positional orthology: putting genomic evolutionary relationships into context. Brief Bioinform. 12(5):401-412.
12. Dufayard J, et al. 2005. Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics 21:2596-2603. (Pubitemid 40852303)
13. Edwards C, et al. 2006. Evolution of the human immunodeficiency virus envelope gene is dominated by purifying selection. Genetics 174(3):1441-1453. (Pubitemid 44808313)
14. Fitch D, et al. 1991. Duplication of the gamma-globin gene mediated by L1 long interspersed repetitive elements in an early ancestor of simian primates. Proc Natl Acad Sci U S A. 88(16):7396-7400. (Pubitemid 21915158)
15. Fitch W. 1970. Distinguishing homologous from analogous proteins. Syst Zool. 19:99-113.
16. Fitch W. 2000. Homology: a personal view on some of the problems. Trends Genet. 16(5):227-231. (Pubitemid 30216555)
17. Gish W, States D. 1993. Identification of protein coding regions by database similarity search. Nat Genet. 3:266-272. (Pubitemid 23096565)
18. Gonzalez E, et al. 2005. The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science 307(5714):1434-1440. (Pubitemid 40321934)
19. Goodstadt L, Ponting C. 2006. Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human. PLoS Comput Biol. 2:e133.
20. *11 while diminishing avidity for HLA-C. J Exp Med. 206(11):2557-2572.
21. Guethlein L, Aguilar AO, Abi-Rached L, Parham P. 2007. Evolution of killer cell Ig-like receptor (KIR) genes: definition of an orangutan KIR haplotype reveals expansion of lineage III KIR associated with the emergence of MHC-C. J Immunol. 179(1):491-504. (Pubitemid 46986566)
22. Guethlein L, Flodin L, Adams E, Parham P. 2002. NK cell receptors of the orangutan (Pongo pygmaeus): a pivotal species for tracking the coevolution of killer cell Ig-like receptors with MHC-C. J Immunol. 169(1):220-229. (Pubitemid 34686139)
23. Han M, Demuth J, McGrath C, Casola C, Hahn M. 2009. Adaptive evolution of young gene duplicates in mammals. Genome Res. 19:859-867.
24. Hardies S, Edgell M, Hutchison C. 1984. Evolution of the mammalian beta-globin gene cluster. J Biol Chem. 259:3748-3756. (Pubitemid 14173414)
25. Hardison R. 1984. Comparison of the beta-like globin gene families of rabbits and humans indicates that the gene cluster 5'-epsilon-gamma-delta-beta- 3' predates the mammalian radiation. Mol Biol Evol. 1:390-410. (Pubitemid 15179353)
26. Hardison R, Gelinas R. 1986. Assignment of orthologous relationships among mammalian alpha-like globin genes by examining flanking regions reveals a rapid rate of evolution. Mol Biol Evol. 3: 243-261. (Pubitemid 16056326)
27. Hardison R, Miller W. 1993. Use of long sequence alignments to study the evolution and regulation of mammalian globin gene clusters. Mol Biol Evol. 10:73-102. (Pubitemid 23040226)
28. Harris R. 2007. Improved pairwise alignment of genomic DNA [PhD thesis]. [University Park (PA)]: Pennsylvania State University.
29. Hoffmann F, Opazo J, Storz J. 2008. Rapid rates of lineage-specific gene duplication and deletion in the α-globin gene family. Mol Biol Evol. 25(3):591-602. (Pubitemid 351301915)
30. Hou M. 2007. Algorithms for aligning and clustering genomic sequences that contain duplications [PhD thesis]. [University Park (PA)]: Pennsylvania State University.
31. Hou M, Riemer C, Berman P, Hardison R, Miller W. 2009. Aligning two genomic sequences that contain duplications. In: Ciccarelli F, Miklos I, editors. Comparative genomics: International Workshop (RE-COMB-CG 2009), volume 5817 of Lecture Notes in Bioinformatics. Budapest, Hungary: Springer. p. 98-110.
32. Hsu C. 2009. Inference of orthologs, while considering gene conversion, to evaluate whole-genome multiple sequence alignments [PhD thesis]. [University Park (PA)]: Pennsylvania State University.
33. Hsu C, et al. 2010. An effective method for detecting gene conversion events in whole genomes. J Comput Biol. 17(9):1281-1297.
34. Hu S, et al. 2008. Evolution of the CYP2ABFGST gene cluster in rat, and a fine-scale comparison among rodent and primate species. Genetica 133:215-226. (Pubitemid 351661616)
35. Huerta-Cepas J, Bueno A, Dopazo J, Gabaldn T. 2008. PhylomeDB: a database for genome-wide collections of gene phylogenies. Nucleic Acids Res. 36:D491-D496. (Pubitemid 351149772)
36. Jensen R. 2001. Orthologs and paralogs - we need to get it right. Genome Biol. 2(8):1002.1-1002.3.
37. Johnson D, McGeoch C. 1993. Network flows and matching: first DIMACS implementation challenge. American Mathematical Society, Providence, RI.
38. Kim K, Sung S, Caetano-Anolles G, Han J, Kim H. 2008. An approach of orthology detection from homologous sequences under minimum evolution. Nucleic Acids Res. 36:e110.
39. Kristensen D, Wolf Y, Mushegian A, Koonin E. 2011. Computational methods for gene orthology inference. Brief Bioinform. 12(5):379-391.
40. Lee Y, et al. 2002. Cross-referencing eukaryotic genomes: tIGR orthologous gene alignments (TOGA). Genome Res. 12:493-502. (Pubitemid 34233026)
41. Levy D, Farcia-Santre A. 2001. The virus battles: iFN induction of the antiviral state and mechanisms of viral evasion. Cytokine Growth Factor Rev. 12:143-156. (Pubitemid 32590836)
42. Li H, et al. 2006. TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res. 34:572-580.
43. Li L, Stoeckert C, Roos D. 2003. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13:2178-2189. (Pubitemid 37161775)
44. *57 supertype alleles influences the progression of HIV-1 infection in a Zambian population. Hum Immunol. 66(3):285-289. (Pubitemid 40395248)
45. Margulies E, et al. 2007. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 17(6):760-764.
46. Martin A, et al. 2004. Comparative genomic analysis, diversity and evolution of two KIR haplotypes A and B. Gene 335:121-131. (Pubitemid 38759758)
47. Matsuya A, et al. 2008. Evola: ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees. Nucleic Acids Res. 36:787-792.
48. Mi H, et al. 2010. PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res. 38:D204-D210.
49. Miyata T, Hayashida H, Kikuno R, Toh H, Kawada Y. 1985. Evolution of interferon genes. Interferon 6:1-30.
50. Muller J, et al. 2010. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res. 38:D190-D195.
51. Murphy W, et al. 2001. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294:2348-2351. (Pubitemid 33140557)
52. Opazo J, Hoffmann F, Storz J. 2008. Differential loss of embryonic globin genes during the radiation of placental mammals. PNAS. 105(35):12950-12955.
53. Opazo J, Sloon A, Campbell K, Storz J. 2009. Origin and ascendancy of a chimeric fusion gene: the b/d-globin gene of paenungulate mammals. Mol Biol Evol. 26(7):1469-1478.
54. Ostlund G, et al. 2010. InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Res. 38:D196-D203.
55. Ouzounis C. 1999. Orthology: another terminology muddle. Trends Genet. 15(11):445. (Pubitemid 29507038)
56. Parham P. 2005. MHC class I molecules and KIRs in human history, health and survival. Nat Rev Immunol. 5(3):201-214. (Pubitemid 40364822)
57. Pianezza M, Sellers E, Tyndale R. 1998. Nicotine metabolism defect reduces smoking. Nature 393:750. (Pubitemid 28299478)
58. Rajalingam R, Parham P, Abi-Rached L. 2004. Domain shuffling has been the main mechanism forming new hominoid killer cell Ig-like receptors. J Immunol. 172(1):356-369. (Pubitemid 38020490)
59. Sambrook J, et al. 2006. Identification of the ancestral killer immunoglobulin-like receptor gene in primates. BMC Genomics 7:209.
60. Shilling H, Lienert-Weidenbach K, Valiante N, Uhrberg M, Parham P. 1998. Evidence for recombination as a mechanism for KIR diversification. Immunogenetics 48:413-416. (Pubitemid 28482587)
61. Siepel A, et al. 2005. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15:1034-1050. (Pubitemid 41126859)
62. Smit A, Hubley R, Green P. 1996-2010. RepeatMasker Open-3.0. [cited 2012 Mar 22] Available from: http://www.repeatmasker.org
63. Song G, Hsu C, Riemer C, Miller W. 2011. Evaluation of methods for detecting conversion events in gene clusters. BMC Bioinfomatics 12(Suppl 1):S45.
64. Song G, et al. 2011. Conversion events in gene clusters. BMC Evol Biol. 11:226.
65. Song G, Zhang L, Vinar T, Miller W. 2010. CAGE: combinatorial analysis of gene-cluster evolution. J Comput Biol. 17:1227-1242.
66. Sonnhammer E, Koonin E. 2002. Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet. 18:619-620. (Pubitemid 35346684)
67. Su T, et al. 2000. Human cytochrome P450 CYP2A13 predominant expression in the respiratory tract and its high efficiency metabolic activation of a tobacco-specific carcinogen, 4(methylnitrosamino)-1-(3-pyridyl)-1-butanone. Cancer Res. 60:5074-5079.
68. Tatusov R, et al. 2001. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29:22-28. (Pubitemid 32054398)
69. The ENCODE Project Consortium 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816.
70. Uchiyama I. 2007. MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups. Nucleic Acids Res. 35:D343-D346. (Pubitemid 46056228)
71. van der Heijden R, Snel B, van Noort V, Huynen M. 2007. Orthology prediction at scalable resolution by phylogenetic tree analysis. Nucleic Acids Res. 8:83.
72. Vilella A, et al. 2009. EnsemblCompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates. Genome Res. 19(2):327-335.
73. Wang H, et al. 2003. Substantial reduction in risk of lung adenocarci-noma associated with genetic polymorphism in CYP2A13, the most active cytochrome P450 for the metabolic activation of tobacco-specific carcinogen NNK. Cancer Res. 63(22):8057-8061. (Pubitemid 37466745)
74. Wapinski I, Pfeffer A, Friedman N, Regev A. 2007. Natural history and evolutionary principlesofgene duplicationinfungi. Nature 449:54-61. (Pubitemid 47373776)
75. Waterhouse R, Zdobnov E, Tegenfeldt F, Li J, Kriventseva E. 2011. OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. Nucleic Acids Res. 36:D271-D275. (Pubitemid 351149735)
76. Wilson D, McVean G. 2006. Estimating diversifying selection and functional constraint in the presence of recombination. Genetics 172:1411-1425.
77. Wilson M, et al. 2000. Plasticity in the organization and sequences of human KIRILT gene families. Proc Natl Acad Sci U S A. 97(9):4778-4783. (Pubitemid 30238634)
78. Woelk C, Frost S, Richman D, Higley P, Pond S. 2007. Evolution of the interferon alpha gene family in eutherian mammals. Gene 397(1-2):38-50. (Pubitemid 46977131)
79. Zhang Y, et al. 2009. Evolutionary history reconstruction for mammalian complex gene clusters. J Comput Biol. 16(8):1051-1070.