Inferring genome-scale rearrangement phylogeny and ancestral gene order: A Drosophila case study

Genome Biology

Volumn 8, Issue 11, 2007, Pages

  Bhutkar, Arjun ^a,b   Gelbart, William M ^b   Smith, Temple F ^a  

^a BOSTON UNIVERSITY   (United States)

^b HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME REARRANGEMENT; CONTROLLED STUDY; DROSOPHILA; GENE CLUSTER; GENE ORDER; GENE REARRANGEMENT; GENOME ANALYSIS; INSECT GENETICS; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; PLESIOMORPHY; SEQUENCE HOMOLOGY; SYNTENY; ALGORITHM; ANIMAL; GENETICS; GENOME; PHYLOGENY; SPECIES DIFFERENCE; STATISTICAL MODEL;

ALGORITHMS; ANIMALS; DROSOPHILA; GENE ORDER; GENOME; LIKELIHOOD FUNCTIONS; PHYLOGENY; SPECIES SPECIFICITY;

EID: 46649120347     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2007-8-11-r236     Document Type: Article

References (73)

1. Bridges CB Salivary chromosome maps with a key to the banding of the chromosomes of Drosophila melanogaster. J Hered 1935 26 60-64
2. Dobzhansky T Microgeographic variation in Drosophila pseudoobscura. Genetics 1939 25 311-314
3. Sturtevant AH Tan CC The comparative genetics of Drosophila pseudoobscura and D. melanogaster. J Genet 1937 34 415-432
4. Sturtevant AH Novitski E The homologies of the chromosome elements in the genus Drosophila. Genetics 1941 26 517-541 1209144 17247021
5. Dobzhansky T Sturtevant AH Inversions in the chromosomes of Drosophila pseudoobscura. Genetics 1938 23 28-64 1209001 17246876
6. Sturtevant AH Dobzhansky T Geographical distribution and cytology of 'sex ratio' in Drosophila pseudoobscura and related species. Genetics 1936 21 473-90 1208687 17246805
7. Sturtevant AH Beadle GW The relations of inversions in the X chromosome of Drosophila melanogaster to crossing over and disjunction. Genetics 1936 21 544-604
8. Sturtevant AH Dobzhansky T Inversions in the third chromosome of wild race of Drosophila pseudoobscura, and their use in the study of the history of the species. Proc Natl Acad Sci USA 1936 22 448 1076803 16577723
9. Muller S Hollatz M Wienberg J Chromosomal phylogeny and evolution of gibbons (Hylobatidae). Hum Genet 2003 113 493-501 14569461
10. Kirkpatrick M Barton N Chromosome inversions, local adaptation, and speciation. Genetics 2006 173 419-434 1461441 16204214
11. White MJD Animal Cytology and Evolution Cambridge: Cambridge University Press 1973
12. Kube M Beck A Zinder SH Kuhl H Reinhardt R Adrian L Genome sequence of the chlorinated compound-respiring bacterium Dehalococcoides species strain CBDB1. Nat Biotechnol 2005 10 1269-1273
13. Richards S Liu Y Bettencourt BR Hradecky P Letovsky S Nielsen R Thornton K Hubisz MJ Chen R Meisel RP et al. Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution. Genome Res 2005 1 1-18
14. Mouse Genome Sequencing Consortium Initial sequencing and comparative analysis of the mouse genome. Nature 2002 420 520-562 12466850
15. Sun HF Ernst CW Yerle M Pinton P Rothschild MF Chardon P Rogel-Gaillard C Tuggle CK Human chromosome 3 and pig chromosome 13 show complete synteny conservation but extensive gene-order differences. Cytogenet Cell Genet 1999 85 273-278 10449917
16. The Chimpanzee Sequencing and Analysis Consortium Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 2005 437 69 87 16136131
17. Dujon B Sherman D Fischer G Durrens P Casaregola S Lafontaine I De Montigny J Marck C Neuveglise C Talla E et al. Genome evolution in yeasts. Nature 2004 430 35-44 15229592
18. International Human Genome Sequencing Consortium Initial sequencing and analysis of the human genome. Nature 2001 409 860 921 11237011
19. Hannenhalli S Pevzner PA Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). Proceedings of the 27th Annual ACM-SIAM Symposium on the Theory of Computing: 1995 1995 178 189 May 29 - June 01, 1995; Editors: F. Tom Leighton, Allan Borodin; Las Vegas, Nevada; ACM Press, New York, NY, USA
20. Kececioglu J Sankoff D Exact and approximation algorithms for sorting by reversals, with application to genome rearrangement. Algorithmica 1995 13 180-210
21. Blanchette M Bourque G Sankoff D Breakpoint phylogenies. Genome inform. ser. workshop. Genome Infor 1997 8 25-34
22. Blanchette M Sankoff D The median problem for breakpoints in comparative genomics. Proceedings of the Third Annual International Conference on Computing and Combinatorics: 1997 Springer Verlag Jiang T, Lee DT 1997 251-263 [Lecture Notes in Computer Science, vol. 1276] August 20-22; Shanghai, China; Springer-Verlag, London, UK
23. Moret BME Tang J Warnow T Reconstructing phylogenies from gene-content and gene-order data. Mathematics of Evolution and Phylogeny Oxford: Oxford University Press Gascuel O 2005 321-352
24. Wang LS Jansen RK Moret BME Raubeson L Warnow T Fast phylogenetic methods for the analysis of genome rearrangement data: An empirical study. Proceedings of the 7th Pacific Symposium on Biocomputing: 2002; Hawaii World Scientific Pub 2002 524-535 January 3-7 2002; Lihue, Hawaii, USA; Editors: Russ B. Altman, A. Keith Dunker, Lawrence Hunter, Teri E. Klein; World Scientific, New Jersey, USA
25. Moret BME Tang J Wang LS Warnow T Steps toward accurate reconstruction of phylogenies from gene-order data. J Comput Syst Sci 2002 65 508-525
26. Caprara A Formulations and hardness of multiple sorting by reversals. Proceedings of the 3rd International Conference on Computational Molecular Biology ACM Press 1999 84-93 April 11-14 1999; Lyon, France; Editors: S. Istrail, P. Pevzner, M. Waterman; ACM Press, New York, NY, USA
27. Pe'er I Shamir R The median problems for breakpoints are NP-complete. Elec Colloq Comput Complexity 1998 71
28. Stanyon R Dumas F Stone G Bigoni F Multidirectional chromosome painting reveals a remarkable syntenic homology between the greater galagos and the slow loris. Am J Primatol 2006 68 349-359 16534804
29. Huynen MA Snel B Bork P Inversions and the dynamics of eukaryotic gene order. Trends Genet 2001 17 304-6 11377779
30. Kaufman TC Severson DW Robinson GE The Anopheles genome and comparative insect genomics. Science 2002 298 97-98 12364783
31. Russo CAM Takezaki N Nei M Molecular phylogeny and divergence times of drosophilid species. Mol Biol Evol 1995 12 391-404 7739381
32. Powell JR Progress and Prospects in Evolutionary Biology: The Drosophila Model New York: Oxford University Press 1997
33. Matthews KA Kaufman TC Gelbart WM Research resources for Drosophila: The expanding universe. Nat Rev Genet 2005 6 179-193 15738962
34. Hartl DL Fly meets shotgun: Shotgun wins. Nat Rev Genet 2000 24 327-328
35. Ranz JM González J Casals A Ruiz A Low occurrence of gene transposition events during the evolution of the genus Drosophila. Int J Org Evolution 2003 57 1325-1335
36. Muller HJ Bearings of the Drosophila work on systematics. The New Systematics Oxford, UK: Clarendon Press Huxley J 1940 185-268
37. Betrán E Thornton K Long M Retroposed new genes out of the X in Drosophila. Genome Res 2002 12 1854-1859 187566 12466289
38. Betrán E Long M Dntf-2r, a young Drosophila retroposed gene with specific male expression under positive Darwinian selection. Genetics 2003 164 977-988 1462638 12871908
39. Ko W David RM Akashi H Molecular phylogeny of the Drosophila melanogaster species subgroup. J Mol Evol 2003 57 562-573 14738315
40. Shibata H Yamazaki T Molecular evolution of the duplicated Amy locus in the Drosophila melanogaster species subgroup: Concerted evolution only in the coding region and an excess of nonsynonymous substitutions in speciation. Genetics 1995 141 223-236 1206720 8536970
41. Jeffs PS Holmes EC Ashburner M The molecular evolution of the alcohol dehydrogenase and alcohol dehydrogenase-related genes in the Drosophila melanogaster species subgroup. Mol Biol Evol 1994 11 287-304 8170369
42. Bergman CM Pfeiffer BD Rincón-Limas DE Hoskins RA Gnirke A Mungall CJ Wang AM Kronmiller B Pacleb J Park S et al. Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome. Genome Biol 2002 3
43. Negre B Casillas S Suzanne M Sánchez-Herrero E Akam M Nefedov M Barbadilla A de Jong P Ruiz A Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex. Genome Res 2005 15 692-700 1088297 15867430
44. Drysdale RA Crosby MA Flybase Consortium FlyBase: Genes and gene models. Nucleic Acids Res 2005 33 Database D390-D395 540000 15608223
45. Ranz JM Casals F Ruiz A How malleable is the eukaryotic genome? Extreme rate of chromosomal rearrangement in the genus Drosophila. Genome Res 2001 2 230-239
46. Lemeunier F Ashburner M Relationships within the melanogaster species subgroup of the genus Drosophila (Sophophora) IV. The chromosomes of two new species. Chromosoma 1984 89 343-351
47. Lemeunier F Ashburner MA Relationships within the melanogaster species subgroup of the genus Drosophila (Sophophora). II. Phylogenetic relationships between six species based upon polytene chromosome banding sequences. Proc R Soc Lond B Biol Sci 1976 193 275-294 6967
48. Bartolome C Maside X Charlesworth B On the abundance and distribution of transposable elements in the genome of Drosophila melanogaster. Mol Biol Evol 2002 19 926-937 12032249
49. Rizzon C Marais G Gouy M Biemont C Recombination rate and the distribution of transposable elements in the Drosophila melanogaster genome. Genome Res 2002 12 400-407 155295 11875027
50. Caceres M Ranz JM Barbadilla A Long M Ruiz A Generation of a widespread Drosophila inversion by a transposable element. Science 1999 285 415-418 10411506
51. Casals F Caceres M Ruiz A The Foldback-like transposon Galileo is involved in the generation of two different natural chromosomal inversions of Drosophila buzzatii. Mol Biol Evol 2003 20 674-685 12679549
52. Casals F Caceres M Manfrin MH Gonzalez J Ruiz A Molecular characterization and chromosomal distribution of Galileo, Kepler and Newton, three foldback transposable elements of the Drosophila buzzatii species complex. Genetics 2005 169 2047-2059 1449584 15695364
53. Evgen'ev MB Zelentsova H Poluectova H Lyozin GT Veleikodvorskaja V Pyatkov KI Zhivotovsky LA Kidwell MG Mobile elements and chromosomal evolution in the virilis group of Drosophila. Proc Natl Acad Sci USA 2000 97 11337-11342 17201 11016976
54. Sankoff D Blanchette M Multiple genome rearrangement and breakpoint phylogeny. J Computational Biol 1998 5 555-570
55. Bourque G Pevzner P Genome-scale evolution: Reconstructing gene orders in the ancestral species. Genome Res 2002 12 26-36 155248 11779828
56. Tesler G GRIMM: Genome rearrangements web server. Bioinformatics 2002 18 492-493 11934753
57. Boore JL MGA Source Guide http://evogen.jgi.doe.gov
58. Boore JL Brown WM Mitochondrial genomes of Galathealinum, Helobdella, and Platynereis: Sequence and gene arrangement comparisons indicate that Pogonophora is not a phylum and Annelida and Arthropoda are not sister taxa. Mol Biol Evol 2000 17 87-106 10666709
59. Bartolome C Charlesworth B Results and patterns of chromosomal evolution in Drosophila pseudoobscura and D. miranda. Genetics 2006 173 773-791
60. Tamura K Subramanian S Kumar S Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol 2004 21 36-44 12949132
61. Cosner ME Jansen RK Moret BME Raubeson LA Wang LS Warnow T Wyman S A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data. Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology: 2000; San Diego 2000 104-115 August 19-23; La Jolla, CA, USA; Editors: Philip Bourne, Michael Gribskov, Russ Altman, Nancy Jensen, Debra Hope, Thomas Lengauer, Julie Mitchell, Eric Scheeff, Chris Smith, Shawn Strande, and Helge Weissig; AAAI Press, CA, USA
62. Cosner ME Jansen RK Moret BME Raubeson LA Wang LS Warnow T Wyman S An emperical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae. Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment, and the Evolution of Gene Families Dordrecht, Netherlands: Kluwer Academic Publishers Sankoff D, Nadeau J 2000 99-121
63. FlyBase http://flybase.org
64. Assembly/Alignment/Annotation of 12 related Drosophila Species http://rana.lbl.gov/drosophila
65. Holt RA Subramanian GM Halpern A Sutton GG Charlab R Nusskern DR Wincker P Clark AG Ribeiro JM Wides R The genome sequence of the malaria mosquito Anopheles gambiae. Science 2002 298 129-149 12364791
66. Ensmbl: Anopheles Gambiae version AgamP3 http://www.ensembl.org/ Anopheles_gambiae
67. Nene V Wortman JR Lawson D Haas B Kodira C Tu Z Loftus B Xi Z Megy K Grabherr M et al. Genome sequence of Aedes Aegypti, a major arbovirus vector. Science 2007 316 1718-1723 17510324
68. Ensmbl: Aedes Aegypti version AaegL1 http://www.ensembl.org/ Aedes_aegypti/index.html
69. BCM: Apis mellifera VFersion 4.0 ftp://ftp.hgsc.bcm.tmc.edu/pub/data/ Amellifera
70. Honeybee Genome Sequencing Consortium Insights into social insects from the genome of the honeybee Apis mellifera. Nature 2006 443 931-949 2048586 17073008
71. BCM: Tribolium castaneum Release 2 http://www.hgsc.bcm.tmc.edu/projects/ tribolium/
72. Bhutkar A Russo S Smith TF Gelbart WM Techniques for multi-genome synteny analysis to overcome assembly limitations. Genome Informatics 2006 17 152-61 17503388
73. Felsenstein J PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 1989 5 164-166