From sequence to chromosome: The tip of the X chromosome of D. melanogaster

Science

Volumn 287, Issue 5461, 2000, Pages 2220-2222

  Benos, Panayiotis V ^a   Gatt, Melanie K ^a   Ashburner, Michael ^a   Murphy, Lee ^a   Harris, David ^a   Barrell, Bart ^a   Ferraz, Conception ^a   Vidal, Sophie ^a   Brun, Christine ^a   Demailles, Jacques ^a   Cadieu, Edouard ^a   Dreano, Stephane ^a   Gloux, Stéphanie ^a   Lelaure, Valerie ^a   Mottier, Stephanie ^a   Galibert, Francis ^a   Borkova, Dana ^a   Minana, Belen ^a   Kafatos, Fotis C ^a   Louis, Christos ^a   Sidén Kiamos, Inga ^a   Bolshakov, Slava ^a   Papagiannakis, George ^a   Spanos, Lefteris ^a   Cox, Sarah ^a   Madueño, Encarnación ^a   De Pablos, Beatriz ^a   Modolell, Juan ^a   Peter, Annette ^a   Schöttler, Petra ^a   Werner, Meike ^a   Mourkioti, Foteini ^a   Beinert, Nicole ^a   Dowe, Gordon ^a   Schäfer, Ulrich ^a   Jäckle, Herbert ^a   Bucheton, Alain ^a   Callister, Deborah M ^a   Campbell, Lorna A ^a   Darlamitsou, Areti ^a   Henderson, Nadine S ^a   McMillan, Paul J ^a   Salles, Cathy ^a   Tait, Evelyn A ^a   Valenti, Phillipe ^a   Saunders, Robert D C ^a   Glover, David M ^a   more..

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

BASE PAIRING; DNA SEQUENCE; DROSOPHILA MELANOGASTER; GENE SEQUENCE; IN SITU HYBRIDIZATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REVIEW; UNINDEXED SEQUENCE; X CHROMOSOME;

ANIMALS; CHROMOSOME BANDING; COMPUTATIONAL BIOLOGY; COSMIDS; DNA TRANSPOSABLE ELEMENTS; DNA, SATELLITE; DROSOPHILA MELANOGASTER; GENES, INSECT; IN SITU HYBRIDIZATION; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA; X CHROMOSOME;

DROSOPHILA MELANOGASTER; MELANOGASTER;

EID: 0034708502     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.287.5461.2220     Document Type: Review

References (33)

1. A. H. Sturtevant, J Exp. Zool. 14, 43 (1913).
2. M. Adams et al., Science 287, 2185 (2000); G. M. Rubin et al., Science 287, 2204 (2000).
3. M. Adams et al., Science 287, 2185 (2000); G. M. Rubin et al., Science 287, 2204 (2000).
4. R. D. C. Saunders et al., Nucleic Acids Res. 17, 9027 (1989); I. Sidén-Kiamos et al., Nucleic Acids Res. 18, 6261 (1990); E. Madueno et al., Genetics 139, 1631 (1995).
5. R. D. C. Saunders et al., Nucleic Acids Res. 17, 9027 (1989); I. Sidén-Kiamos et al., Nucleic Acids Res. 18, 6261 (1990); E. Madueno et al., Genetics 139, 1631 (1995).
6. R. D. C. Saunders et al., Nucleic Acids Res. 17, 9027 (1989); I. Sidén-Kiamos et al., Nucleic Acids Res. 18, 6261 (1990); E. Madueno et al., Genetics 139, 1631 (1995).
7. P. V. Benos et al., in preparation; A. Peter et al., in preparation. The sequence was determined from a minimum tiling path of the cosmid and bacterial artificial chromosome (BAC) clones that had been used to construct a physical map of the X chromosome (6). Two BAC libraries were made by Alain Billaud at the Centre d'Etude du Polymorphisme Humaine in a collaboration with the EDGP and one was obtained from the Berkeley Drosophila Genome Project [R. A. Hoskins et al., Science 287, 2271 (2000)]. A BAC, Ndel (BACN) library was prepared with Nde II inserts and a BAC, Hind II (BACH) library with Hind III inserts in the vector pBeloBACII. These libraries were made with pools of size-fractionated DNA that gives mean insert sizes of up to 90 kb. The 23,400 clones give about a 10-fold coverage of the genome. These libraries are available at www.hgmp.mrc.ac.uk/Biology/ Bio.html. Sequence-tagged sites of both terminal insert sequences were determined for a total of about 5350 BACs from these libraries (www.genoscope.cns.fr/ externe/English/Projets/Resultats/rapport.html). The assembled nonredundant 2.6 Mb sequence is at edgp. ebi.ac.uk/cgi-bin/progress.pl, which links to the following European Molecular Biology Laboratory database accession numbers: AL009146, AL009147, L009171, AL009188-AL009196, AL021067, AL021086, AL021106 to AL021108, AL021726, AL021728, AL022017, AL022018, AL022139, AL023873, AL023874, AL023893, AL024453-AL024457, AL024484, AL024485, AL030993, AL030994, AL031024-AL031131, AL031173, AL031227, AL031366, AL031367, AL031581-AL031583, AL031640, AL031765, AL031766, AL031863, AL031883, AL031884, AL033125, AL034388, AL034544, AL035104, AL035105, AL035207, AL03524S, AL035311, AL035312, AL035331, AL035395, AL035436, AL035631, AL035632, AL049535, AI050231, AL050232, AL109630, AL121800, AL121803-AL121806, AL132651, A1132792, AL132797, AL133503 to AL133506, AL138678, AL138971, AL138972, Z98254, and Z98269. Sequences were analyzed by methods similar to those described (6). Data were managed with AceDB.
8. T. H. Morgan, Science 32, 120 (1910); C. B. Bridges, Genetics 1, 1, 107 (1916).
9. T. H. Morgan, Science 32, 120 (1910); C. B. Bridges, Genetics 1, 1, 107 (1916).
10. M. Ashburner et al., Genetics 153, 179 (1999).
11. C. H. Langley, E. A. Montgomery, R. Hudson, N. L. Kaplan, B. Charlesworth, Genet. Res. 52, 223 (1988); B. Charlesworth and A. Lapid, Genet. Res. 54, 113 (1989); P. D. Sniegowski and B. Charlesworth, Genetics 137, 815 (1994); C. Hoogland and C. Biemont, Genetics 144, 197 (1996).
12. C. H. Langley, E. A. Montgomery, R. Hudson, N. L. Kaplan, B. Charlesworth, Genet. Res. 52, 223 (1988); B. Charlesworth and A. Lapid, Genet. Res. 54, 113 (1989); P. D. Sniegowski and B. Charlesworth, Genetics 137, 815 (1994); C. Hoogland and C. Biemont, Genetics 144, 197 (1996).
13. C. H. Langley, E. A. Montgomery, R. Hudson, N. L. Kaplan, B. Charlesworth, Genet. Res. 52, 223 (1988); B. Charlesworth and A. Lapid, Genet. Res. 54, 113 (1989); P. D. Sniegowski and B. Charlesworth, Genetics 137, 815 (1994); C. Hoogland and C. Biemont, Genetics 144, 197 (1996).
14. C. H. Langley, E. A. Montgomery, R. Hudson, N. L. Kaplan, B. Charlesworth, Genet. Res. 52, 223 (1988); B. Charlesworth and A. Lapid, Genet. Res. 54, 113 (1989); P. D. Sniegowski and B. Charlesworth, Genetics 137, 815 (1994); C. Hoogland and C. Biemont, Genetics 144, 197 (1996).
15. C. B. Bridges, J. Hered. 26, 60 (1935).
16. _, Cytologia (Fujii Jubilee Vol.) 745 (1937).
17. There have been many studies of polytene chromosome banding patterns in related species. Perhaps the most complete is that of the Hawaiian fauna; see H. L. Carson J. Tonzetich, L. T. Doescher, in Drosophila Inversion Polymorphism, C. B. Krimbas and J. R. Powell, Eds. (CRC, Boca Raton, FL, 1992), pp. 441-453. For the persistence of banding patterns over long evolutionary time, see H. D. Stalker, Genetics 70, 457 (1972).
18. There have been many studies of polytene chromosome banding patterns in related species. Perhaps the most complete is that of the Hawaiian fauna; see H. L. Carson J. Tonzetich, L. T. Doescher, in Drosophila Inversion Polymorphism, C. B. Krimbas and J. R. Powell, Eds. (CRC, Boca Raton, FL, 1992), pp. 441-453. For the persistence of banding patterns over long evolutionary time, see H. D. Stalker, Genetics 70, 457 (1972).
19. V. Sorsa, Chromosome Maps of Drosophila: vols. 1 and 2 (CRC, Boca Raton, FL, 1988).
20. C. B. Bridges, J. Hered. 29, 11 (1938).
21. C. A. Offermann, J. Genet. 32, 102 (1936).
22. See figure 17.2 of M. Ashburner, Drosophila: A Laboratory Handbook (Cold Spring Harbor Press, Cold Spring Harbor, NY, 1989); D. Gubb, M. Ashburner, J. Roote, T. Davis, Genetics 126, 167 (1990).
23. See figure 17.2 of M. Ashburner, Drosophila: A Laboratory Handbook (Cold Spring Harbor Press, Cold Spring Harbor, NY, 1989); D. Gubb, M. Ashburner, J. Roote, T. Davis, Genetics 126, 167 (1990).
24. C. D. Kastritsis, Z. G. Scouras, M. Ashburner, Chromosoma 93, 381 (1986).
25. I. F. Zhimulev, E. S. Belyaeva, O. M. Mazina, M. C. Balasov, Eur. J. Entomol. 92, 263 (1992); G. Tzolovsky, W.-M. Deng, T. Schlitt, M. Bownes, Genetics 153, 1371 (1999).
26. I. F. Zhimulev, E. S. Belyaeva, O. M. Mazina, M. C. Balasov, Eur. J. Entomol. 92, 263 (1992); G. Tzolovsky, W.-M. Deng, T. Schlitt, M. Bownes, Genetics 153, 1371 (1999).
27. H. J. Becker, Chromosoma 10, 654 (1959).
28. Methods for repeat analysis used were DOTTER [E. L. L. Sonnhammer and R. Durbin, Gene 167, GC1 (1995)] and MIROREPEATS [J. D. Parsons, Comput. Appl. Biosci. 11, 615 (1995)]. Sequence alignments were made with CLUSTALW [J. D. Thompson, D. G. Higgins, T. J. Gibson, Nucleic Acids Res. 22, 4573 (1994)].
29. Methods for repeat analysis used were DOTTER [E. L . L. Sonnhammer and R. Durbin, Gene 167, GC1 (1995)] and MIROREPEATS [J. D. Parsons, Comput. Appl. Biosci. 11, 615 (1995)]. Sequence alignments were made with CLUSTALW [J. D. Thompson, D. G. Higgins, T. J. Gibson, Nucleic Acids Res. 22, 4573 (1994)].
30. Methods for repeat analysis used were DOTTER [E. L. L. Sonnhammer and R. Durbin, Gene 167, GC1 (1995)] and MIROREPEATS [J. D. Parsons, Comput. Appl. Biosci. 11, 615 (1995)]. Sequence alignments were made with CLUSTALW [J. D. Thompson, D. G. Higgins, T. J. Gibson, Nucleic Acids Res. 22, 4573 (1994)].
31. G. L. Waring and J. C. Pollack, Proc. Natl. Acad. Sci. U.S.A. 64, 2843 (1987); S. M. DiBartolomeis, K. D. Tartof, F. R. Jackson, Nucleic Acids Res. 20, 1113 (1992).
32. G. L. Waring and J. C. Pollack, Proc. Natl. Acad. Sci. U.S.A. 64, 2843 (1987); S. M. DiBartolomeis, K. D. Tartof, F. R. Jackson, Nucleic Acids Res. 20, 1113 (1992).
33. We thank the European Commission for financial support under the Biotechnology Programme of Framework 4. This work was also supported by a Medical Research Council (UK) project grant to D.M.G. and M.A. and by a Dirección General de Investigación Cientlfica y Técnica grant to J.M. Work in Göttingen was supported by the Deutsche Humangenomprojekt. R.D.C.S. held a Wellcome Trust Senior Fellowship. We thank G. M. Rubin and his colleagues in the Berkeley Drosophila Genome Project for their long-standing collaboration and, in particular, for their BAC, Eco RI (BACR) clone library and their expressed sequence tag and EP-element sequences. We thank R. Durbin and his colleagues in the Sanger Centre for help with ACeDB.