The genome sequence of the malaria mosquito Anopheles gambiae

Science

Volumn 298, Issue 5591, 2002, Pages 129-149

  Holt, R A ^a,t   Mani Subramanian, G ^a   Halpern, A ^a   Sutton, G G ^a   Charlab, R ^a   Nusskern, D R ^a   Wincker, P ^b   Clark, A G ^c   Ribeiro, J M C ^d   Wides, R ^e   Salzberg, S L ^f   Loftus, B ^f   Yandell, M ^a   Majoros, W H ^a,f   Rusch, D B ^a   Lai, Z ^a   Kraft, C L ^a   Abril, J F ^g   Anthouard, V ^b   Arensburger, P ^h   Atkinson, P W ^h   Baden, H ^a   de Berardinis, V ^b   Baldwin, D ^a   Benes, V ⁱ   Biedler, J ^j   Blass, C ⁱ   Bolanos, R ^a   Boscus, D ^b   Barnstead, M ^a   Cai, S ^a   Center, A ^a   Chatuverdi, K ^a   Christophides, G K ⁱ   Chrystal, M A ^k   Clamp, M ^l   Cravchik, A ^a   Curwen, V ^l   Dana, A ^k   Delcher, A ^a   Dew, I ^a   Evans, C A ^a   Flanigan, M ^a   Grundschober Freimoser, A ^m   Friedli, L ^h   Gu, Z ^a   Guan, P ^a   Guigo, R ^g   Hillenmeyer, M E ^k   Hladun, S L ^a   Hogan, J R ^k   Hong, Y S ^k   Hoover, J ^a   Jaillon, O ^b   Ke, Z ^a,k   Kodira, C ^a   Kokoza, E ⁿ   Koutsos, A ^o,p   Letunic, I ⁱ   Levitsky, A ^a   Liang, Y ^a   Lin, J J ^p   Lobo, N F ^k   Lopez, J R ^a   Malek, J A ^f,u   McIntosh, T C ^a   Meister, S ⁱ   Miller, J ^a   Mobarry, C ^a   Mongin, E ^q   Murphy, S D ^a   O'Brochta, D A ^m   Pfannkoch, C ^a   Qi, R ^a   Regier, M A ^a   Remington, K ^a   Shao, H ^j   Sharakhova, M V ^k   Sitter, C D ^a   Shetty, J ^f   Smith, T J ^a   Strong, R ^a   Sun, J ^a   Thomasova, D ⁱ   Ton, L Q ^k   Topalis, P ^o,p   Tu, Z ^j   Unger, M F ^k   Walenz, B ^a   Wang, A ^a   Wang, J ^a   Wang, M ^a   Wang, X ^k,v   Woodford, K J ^a   Wortman, J R ^a,f   Wu, M ^f   Yao, A ^a   Zdobnov, E M ⁱ   Zhang, H ^a   Zhao, Q ^a   Zhao, S ^f   Zhu, S C ^a   Zhimulev, I ⁿ   Coluzzi, M ^r   della Torre, A ^r   Roth, C W ^s   Louis, C ^o,p   Kalush, F ^a   Mural, R J ^a   Myers, E W ^a   Adams, M D ^a   Smith, H O ^a   Broder, S ^a   Gardner, M J ^f   Fraser, C M ^f   Birney, E ^q   Bork, P ⁱ   Brey, P T ^s   Craig Venter, J ^a,f   Weissenbach, J ^b   Kafatos, F C ⁱ   Collins, F H ^k   Hoffman, S L ^a,w   more..

^a CELERA GENOMICS   (United States)

^b CENTRE NATIONAL DE SÉQUENÇAGE   (France)

^c Department of Obstetrics Gynecology   (United States)

^d NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

^e BAR ILAN UNIVERSITY   (Israel)

^f J CRAIG VENTER INSTITUTE   (United States)

^g INST MUNIC D INVESTIGACIO MEDICA   (Spain)

^h UNIVERSITY OF CALIFORNIA   (United States)

ⁱ EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^j VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

^k UNIVERSITY OF NOTRE DAME   (United States)

^l WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^m UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

ⁿ INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

^o INSTITUTE OF COMPUTER SCIENCE   (Greece)

^p UNIVERSITY OF CRETE   (Greece)

^q EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^r SAPIENZA UNIVERSITY OF ROME   (Italy)

^s INSTITUT PASTEUR   (France)

^t BRITISH COLUMBIA CANCER AGENCY   (Canada)

^u Agencourt Bioscience Corporation   (United States)

^v SUN YAT SEN UNIVERSITY   (China)

^w SANARIA INC   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

POLYMORPHISM;

BLOOD; CELLS; DISEASES; GENETIC ENGINEERING; IMMUNOLOGY;

GENES;

PROTEOME;

DISEASE CONTROL; GENOME; IMMUNITY; MALARIA; MOSQUITO;

ADAPTATION; ANOPHELES GAMBIAE; ARTICLE; CELL ADHESION; DISEASE CARRIER; EXPRESSED SEQUENCE TAG; GENE CONTROL; GENE SEQUENCE; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC VARIABILITY; HETEROZYGOSITY; IMMUNITY; INSECT GENETICS; MALARIA; NONHUMAN; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; ANOPHELES; BLOOD; CHROMOSOMES, ARTIFICIAL, BACTERIAL; COMPUTATIONAL BIOLOGY; DIGESTION; DNA TRANSPOSABLE ELEMENTS; DROSOPHILA MELANOGASTER; ENZYMES; EVOLUTION; EXPRESSED SEQUENCE TAGS; FEEDING BEHAVIOR; GENE EXPRESSION REGULATION; GENES, INSECT; GENOME; HAPLOTYPES; HUMANS; INSECT PROTEINS; INSECT VECTORS; INVERSION, CHROMOSOME; MALARIA, FALCIPARUM; MOLECULAR SEQUENCE DATA; MOSQUITO CONTROL; PHYSICAL CHROMOSOME MAPPING; PLASMODIUM FALCIPARUM; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEOME; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; TRANSCRIPTION FACTORS; VARIATION (GENETICS);

ANOPHELES GAMBIAE; HEXAPODA; INSECTA;

EID: 0037020114     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.1076181     Document Type: Article

References (61)

1. J. G. Breman, A. Egan, G. T. Keusch, Am. J. Trop. Med. Hyg. 64 (suppl.), 1 (2001).
2. M. Coluzzi, A. Sabantini, V. Petrarca, M. A. Di Deco, Trans. R. Soc. Trop. Med. Hyg. 73, 483 (1979).
3. M. Coluzzi, V. Petrarca, M. A. Di Deco, Boll. Zool. 52, 45 (1985).
4. A. della Torre et al., Insect Mol. Biol. 10, 9 (2001).
5. Y. T. Touré et al., Parassitologia 40, 477 (1998).
6. O. Mukabayire, N. J. Besansky, Chromosoma 104, 585 (1996).
7. G. F. Mason, Genet. Res. 10, 205 (1967).
8. See supporting data on Science Online.
9. A. K. Githeko et al., Trans R. Soc. Trop. Med. Hyg. 86, 355 (1992).
10. H. R. Crollius et al., Genome Res. 10, 939 (2000).
11. S. Zhao et al., Genome Res. 11, 1736 (2001).
12. J. C. Venter et al., Science 291, 1304 (2001).
13. M. D. Adams et al., Science 287, 2185 (2000).
14. E. W. Myers et al., Science 287, 2196 (2000).
15. R. J. Mural et al., Science 296, 1661 (2002).
16. A mate pair is a set of two sequence reads derived from either end of a clone insert such that their relative orientation and distance apart are known.
17. Unitigs are sets of sequence reads that have been uniquely assembled into a single contiguous sequence such that no fragment in the unitig overlaps a fragment not in the unitig. The depth of reads in a unitig and the mate pair structure between it and other unitigs are used to determine whether a given unitig has single or multiple copies in the genome. We define contigs as sets of overlapping unitigs. Unlike scaffolds, which comprise ordered and oriented contigs, unitigs and contigs do not have internal gaps.
18. A nucleotide position was considered to be a SND if the respective column of the multialignment satisfied the following three criteria. First, two different bases (A, C, G, T, or unknown) had to be observed, each in at least two fragments. Second, the total number of fragments covering the column had to be ≤15 [halfway between single (10x) and double (20x) coverage] to reduce the frequency of false positives resulting from overcollapsed repeats. Third, we eliminated all but one of a run of adjacent SND columns so that block mismatches or (more likely) block indels (insertions/deletions) were counted only once.
19. SND "balance" is the ratio of the number of fragments showing the second most frequent character in a column to the number showing the most frequent character.
20. SND "association" shows, for a sliding window of 100 kb, the fraction of polymorphic columns that can be partitioned into two consistent haplotypes. For an SND column A of the multiple sequence alignment and the previous such column B, each fragment might have one of four possible haplotype phases: AB, Ab, aB, or ab, where the upper- and lowercase letters indicate alternative nucleotides. We say that columns A and B are consistent if only two of these four haplotypes are present. For the test to be non-trivial, we require that at least two fragments be observed with each of the two haplotype phases.
21. C. F. Aquadro, A. L. Weaver, S. W. Schaeffer, W. W. Anderson, Proc. Natl. Acad. Sci. U.S.A. 88, 305 (1991).
22. R. Wang, L. Zheng, Y. T. Touré, T. Dandekar, F. C. Kafatos, Proc. Natl. Acad. Sci. U.S.A. 98, 10769 (2001).
23. D. J. Begun, P. Whitley, Proc. Natl. Acad. Sci. U.S.A. 97, 5960 (2000).
24. P. Andolfatto, Mol. Biol. Evol. 18, 279 (2001).
25. D. Thomasová et al., Proc, Natl. Acad. Sci. U.S.A. 99, 8179 (2002).
26. N. J. Besansky, J. R. Powell, J. Med. Entomol. 29, 125 (1992).
27. M. Ashburner, Drosophila: A Laboratory Handbook (Cold Spring Harbor Laboratory Press, Plainview, NY, 1989), p. 74.
28. F. H. Collins, unpublished data.
29. J. M. Comeron, Curr. Opin. Genet. Dev. 1, 652 (2001).
30. D. L. Hartl, Nature Rev. Genet. 1, 145 (2000).
31. C. Rizzon, G. Marais, M. Gouy, C. Biemont, Genome Res. 12, 400 (2002).
32. A. J. Cornel, F. H. Collins, J. Hered, 91, 364 (2000).
33. On the basis of empirical tests, homologous proteins were required to be one of the five best mutual Blast hits within the entire genome, to fall within 15 gene calls of the closest neighboring pair, and to consist of three or more spatial matches.
34. The C. elegans Sequencing Consortium, Science 282, 2012 (1998).
35. S. Aparicio et al., Science 297, 1302 (2002).
36. S. L. Salzberg, R. Wides, unpublished data.
37. E. M. Zdobnov et al., Science 298, 149 (2002).
38. R. Apweiler et al., Nucleic Acids Res, 29, 37 (2001).
39. E. M. Zdobnov, R. Apweiler, Bioinformatics 17, 847 (2001).
40. G. M. Rubin et al., Science 287, 2204 (2000).
41. The complete hierarchy of InterPro entries is described at www.ebi.ac.uk/interpro; the hierarchy for GO is described at www,geneontology.org.
42. M. J. Gorman, S. M. Paskewitz, Insect Biochem. Mol. Biol. 31, 257 (2001).
43. G. Dimopoulos et al., Proc. Natl. Acad. Sci. U.S.A. 97, 6619 (2000).
44. M. Matsushita, T. Fujita, Immunol. Rev. 180, 78 (2001).
45. R. Le Borgne, Y. Bellaiche, F. Schweisguth, Curr. Biol. 12, 95 (2002).
46. C. H. Lee, T. Herman, T. R. Clandinin, R. Lee, S. L. Zipursky, Neuron 30, 437 (2001).
47. S. Ansieau, A. Leutz, J. Biol. Chem. 277, 4906 (2002).
48. D. K. Yeates, B. M. Wiegmann, Annu. Rev. Entomol. 44, 397 (1999).
49. A. N. Clements, Biology of Mosquitoes, Vol. I: Development, Nutrition, Reproduction (Chapman & Hall, Wallingford, UK, 1992).
50. G. Dimopoulos et al., Proc. Natl. Acad. Sci. U.S.A. 99, 8814 (2002).
51. H. Ranson et al., Insect Mol. Biol. 9, 499 (2000).
52. H. Ranson et al., Science 298, 179 (2002).
53. H. Ranson et al., Biochem. J. 359, 295 (2001).
54. C. A. Hill et al., Science 298, 176 (2002).
55. G. Dimopoulos, H. M. Muller, E. A. Levashina, F. C. Kafatos, Curr. Opin. Immunol. 13, 79 (2001).
56. G. K. Christophides et al., Science 298, 159 (2002).
57. F. H. Collins et al., Science 234, 607 (1986).
58. J. Ito, A. Ghosh, L. A. Moreira, E. A. Wimmer, M. Jacobs-Lorena, Nature 417, 452 (2002).
59. L. Zheng et al., Science 276, 425 (1997).
60. J. F. Abril, R. Guigó, Bioinformatics 16, 743 (2000).
61. Supported in part by NIH grant U01AI50687 (R.A.H.) and grants U01AI48846 and R01AI44273 (F.H.C.) on behalf of the Anopheles gambiae Genome Consortium, and by the French Ministry of Research. We thank K. Aultman (NIAID) for her insights and effective coordination, D. Lilley (Celera) for competent financial and administrative management, and all members of the sequencing and support teams at the sequencing centers Celera, Genoscope, and TIGR.