The DNA sequence of chromosome I of an African trypanosome: Gene content, chromosome organisation, recombination and polymorphism

Nucleic Acids Research

Volumn 31, Issue 16, 2003, Pages 4864-4873

  Hall, Neil ^e   Berriman, Matthew ^e   Lennard, Nicola J ^e   Harris, Barbara R ^e   Hertz Fowler, Christiane ^e   Bart Delabesse, Emmanuelle N ^a   Gerrard, Caroline S ^a   Atkin, Rebecca J ^e   Barron, Andrew J ^e   Bowman, Sharen ^e,f   Bray Allen, Sarah P ^e   Bringaud, Frédéric ^b   Clark, Louise N ^e   Corton, Craig H ^e   Cronin, Ann ^e   Davies, Robert ^e   Doggett, Jonathon ^e   Fraser, Audrey ^e   Grüter, Eric ^a   Hall, Sarah ^e   Harper, A David ^e   Kay, Mike P ^e   Leech, Vanessa ^a   Mayes, Rebecca ^e   Price, Claire ^e   Quail, Michael A ^e   Rabbinowitsch, Ester ^e   Reitter, Christopher ^b   Rutherford, Kim ^e   Sasse, Jürgen ^a   Sharp, Sarah ^e   Shownkeen, Ratna ^e   MacLeod, Annette ^c   Taylor, Sonya ^c   Tweedie, Alison ^c   Turner, C Michael R ^c   Tait, Andrew ^c   Gull, Keith ^d   Barrell, Bart ^e   Melville, Sara E ^a   more..

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITÉ DE BORDEAUX   (France)

^c UNIVERSITY OF GLASGOW   (United Kingdom)

^d UNIVERSITY OF OXFORD   (United Kingdom)

^e WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^f JEALOTT S HILL INTERNATIONAL RESEARCH CENTRE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GLYCOPROTEIN;

AFRICA; AFRICAN TRYPANOSOMIASIS; ARTICLE; CHROMOSOME 1; CHROMOSOME STRUCTURE; CONTROLLED STUDY; CROSSING OVER; DNA SEQUENCE; GENE AMPLIFICATION; GENE CLUSTER; GENE CONVERSION; GENE EXPRESSION; GENE FREQUENCY; GENE FUNCTION; GENE INSERTION; GENE LOCATION; GENETIC ANALYSIS; GENETIC CODE; GENETIC POLYMORPHISM; GENETIC RECOMBINATION; GENETIC VARIABILITY; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROTOZOAL GENETICS; PSEUDOGENE; RETROPOSON; SEQUENCE HOMOLOGY; TELOMERE; TRYPANOSOMA BRUCEI;

ANIMALS; CHROMOSOME MAPPING; CHROMOSOMES; DNA, PROTOZOAN; GENES, PROTOZOAN; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; POLYMORPHISM, GENETIC; RECOMBINATION, GENETIC; SEQUENCE ANALYSIS, DNA; TRYPANOSOMA BRUCEI BRUCEI; VARIANT SURFACE GLYCOPROTEINS, TRYPANOSOMA;

INSERTION SEQUENCES; PROTOZOA; TRYPANOSOMA; TRYPANOSOMA BRUCEI;

EID: 10744222662     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg674     Document Type: Article

References (56)

1. World Health Organisation (1998) Control and surveillance of African trypanosomiasis. Report of a WHO expert committee. Technical Report Series, 881.
2. Smith,D.H., Pepin,J. and Stich,A.H.R. (1998) Human African trypanosomiasis: an emerging public health crisis. Brit. Med. Bull., 54, 341-355.
3. Swallow,B.M. (2000) Impacts of trypanosomiasis on African agriculture. PAAT Technical and Scientific Series, FAO, 2.
4. Barrett,M.P. (2001) Veterinary link to drug resistance in human African trypanosomiasis? Lancet, 358, 603-604.
5. Legros,D., Ollivier,G., Gastellu-Etchegorry,M., Paquet,C., Burri,C., Jannin,J. and Büscher,P. (2002) Treatment of human African trypanosomiasis - present situation and needs for research and development. Lancet Infect. Dis., 2, 437-440.
6. Melville,S.E., Leech,V., Gerrard,C.S., Tait,A. and Blackwell,J.M. (1998) The molecular karyotype of the megabase chromosomes of Trypanosoma brucei and the assignment of chromosome markers. Mol. Biochem. Parasit., 94, 155-173.
7. Clayton,C.E. (2002) Life without transcriptional control? From fly to man and back again. EMBO J., 21, 1881-1888.
8. MacLeod,A., Tweedie,A., Welburn,S.C., Maudlin,I., Turner,C.M.R. and Tait,A. (2000) Minisatellite marker analysis of Trypanosoma brucei: Reconciliation of clonal, panmictic and epidemic population genetic structures. Proc. Natl Acad. Sci. USA, 97, 13442-13447.
9. Gibson,W. and Stevens,J. (1999) Genetic exchange in the trypanosomatidae. Adv. Parasit., 43, 1-46.
10. Barry,J.D. and McCulloch,R. (2001) Antigenic variation in trypanosomes: Enhanced phenotypic variation in a eukaryotic parasite. Adv. Parasitol., 49, 1-70.
11. LaCount,D.J., El-Sayed,N.M., Kaul,S., Wanless,D., Turner,C.M.R. and Donelson,J.E. (2001) Analysis of a donor gene region for a variant surface glycoprotein and its expression site in African trypanosomes. Nucleic Acids Res., 29, 2012-2019.
12. Bringaud,F., Biteau,N., Donelson,J.E. and Baltz,T. (2001) Conservation of metacyclic variant surface glycoprotein expression sites among different trypanosome isolates. Mol. Biochem. Parasit., 113, 67-78.
13. Berriman,M., Hall,N., Sheader,K., Bringaud,F.D., Tiwari,B., Isobe,T., Bowman,S., Corton,C., Clark,L., Cross,G.A.M. et al. (2002) The architecture of variant surface glycoprotein gene expression sites in Trypanosoma brucei. Mol. Biochem. Parasit., 122, 131-140.
14. El-Sayed,N.M.A., Ghedin,E., Song,J., MacLeod,A., Bringaud,F., Larkin,C., Wanless,D., Peterson,J., Hou,L., Taylor,S. et al. (2003) The sequence and analysis of Trypanosoma brucei chromosome II. Nucleic Acids Res., 31, 4856-4863.
15. Melville,S.E., Leech,V., Navarro,M. and Cross,G.A.M. (2000) The molecular karyotype of the megabase chromosomes of Trypanosoma brucei stock 427. Mol. Biochem. Parasit., 111, 261-273.
16. Tait,A., Masiga,D., Ouma,J., MacLeod,A., Sasse,J., Melville,S., Lindegard,G., McIntosh,A. and Turner,M. (2002) Genetic analysis of phenotype in Trypanosoma brucei: a classical approach to potentially complex traits. Phil. Trans. Royal Soc. B, 357, 89-99.
17. van Deursen,F.J., Shahi,S.K., Turner,C.M.R., Hartmann,C., Guerra-Giraldez,C., Matthews,K.R. and Clayton,C.E. (2001) Characterisation of the growth and differentiation in vivo and in vitro of bloodstream-form Trypanosoma brucei strain TREU 927. Mol. Biochem. Parasit., 112, 163-171.
18. Melville,S.E., Gerrard,C.S. and Blackwell,J.M. (1999) Multiple causes of size variation in the diploid megabase chromosomes of African trypanosomes. Chromosome Res., 7, 191-203.
19. Bowman,S., Lawson,D., Basham,D., Brown,D., Chillingworth,T., Churcher,C.M., Craig,A., Davies,R.M., Devlin,K., Feltwell,T. et al. (1999) The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum. Nature, 400, 532-538.
20. Rutherford,K., Parkhill,J., Crook,J., Horsnell,T., Rice,P., Rajandream,M.A. and Barrell,B. (2000) Artemis: sequence visualization and annotation. Bioinformatics, 16, 944-945.
21. Delcher,A.L., Harmon,D., Kasif,S., White,O. and Salzberg,S.L. (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res., 27, 4636-4641.
22. Apweiler,R., Attwood,T.K., Bairoch,A., Bateman,A., Birney,E., Biswas,M., Bucher,P., Cerutti,T., Corpet,F., Croning,M.D.R. et al. (2001) The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res., 29, 37-40.
23. Bateman,A., Birney,E., Cerruti,L., Durbin,R., Etwiller,L., Eddy,S.R., Griffiths-Jones,S., Howe,K.L., Marshall,M. and Sonnhammer,E.L.L. (2002) The Pfam Protein Families Database. Nucleic Acids Res., 30, 276-280.
24. Nielsen,H., Brunak,S. and von Heijne,G. (1999) Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Protein Eng., 12, 3-9.
25. Krogh,A., Larsson,B., von Heijne,G. and Sonnhammer,E.L.L. (2001) Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol., 305, 567-580.
26. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. (2000) Gene Ontology: tool for the unification of biology. Nature Genet., 25, 25-29.
27. Sonnhammer,E.L.L. and Durbin,R. (1995) A dot-matrix program with dynamic threshold control suited for genomic DNA and protein-sequence analysis. Gene-Combis, 167, 1-10.
28. Benson,G. (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res., 27, 573-580.
29. Kruglyak,S., Durrett,R.T., Schug,M.D. and Aquadro,C.F. (1998) Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. Proc. Natl Acad. Sci. USA, 95, 10774-10778.
30. Turner,C.M.R., Sternberg,J., Buchanan,N., Smith,E., Hide,G. and Tait,A. (1990) Evidence that the mechanism of gene exchange in Trypanosoma brucei involves meiosis and syngamy. Parasitology, 101, 377-386.
31. Munoz-Jordan,J.L., Cross,G.A.M., de Lange,T. and Griffith,J.D. (2001) T-loops at trypanosome telomeres. EMBO J., 20, 579-588.
32. 90. Nucleic Acids Res., 12, 2759-2774.
33. Berriman,M., Aslett,M., Hall,N. and Ivens,A. (2001) Parasites are GO. Trends Parasitol., 17, 463-464.
34. Gardner,M.J., Hall,N., Fung,E., White,O., Berriman,M., Hyman,R.W., Carlton,J.M., Pain,A., Nelson,K.E., Bowman,S. et al. (2002) Genome sequence of the human malaria parasite Plasmodium falciparum. Nature, 419, 498-511.
35. Myler,P.J., Audleman,L., DeVos,T., Hixson,G., Kiser,P., Lemley,C., Magness,C., Rickel,E., Sisk,E., Sunkin,S. et al. (1999) Leishmania major Friedlin chromosome 1 has an unusual distribution of protein-coding genes. Proc. Natl Acad. Sci. USA, 96, 2902-2906.
36. Tschudi,C. and Ullu,E. (1988) Polygene transcripts are precursors to calmodulin messenger RNAs in trypanosomes. EMBO J., 7, 455-463.
37. Gilinger,G. and Bellofatto,V. (2001) Trypanosome spliced leader RNA genes contain the first identified RNA polymerase II gene promoter in these organisms. Nucleic Acids Res., 29, 1556-1564.
38. Bringaud,F., Vedrenne,C., Cuvillier,A., Parzy,D., Baltz,D., Tetaud,E., Pays,E., Venegas,J., Merlin,G. and Baltz,T. (1998) Conserved organization of genes in trypanosomatids. Mol. Biochem. Parasit., 94, 249-264.
39. Bringaud,F., Biteau,N., Melville,S.E., Hez,S., El-Sayed,N.M., Leech,V., Berriman,M., Hall,N., Donelson,J.E. and Baltz,T. (2002) A new, expressed multigene family containing a hot spot for insertion of retroelements is associated with polymorphic subtelomeric regions of Trypanosoma brucei. Eukaryot. Cell, 1, 315-315.
40. Harrison,P.M. and Gerstein,M. (2002) Studying genomes through the aeons: protein families, pseudogenes and proteome evolution. J. Mol. Biol., 318, 1155-1174.
41. Wilson,R.K. (1999) How the worm was won - the C. elegans genome sequencing project. Trends Genet., 15, 51-58.
42. Winzeler,E.A., Lee,B., McCusker,J.H. and Davis,R.W. (1999) Whole genome genetic-typing in yeast using high-density oligonucleotide arrays. Parasitology, 118, 73-80.
43. Pham,V.P., Rothman,P.B. and Gottesdiener,K.M. (1997) Binding of trans-acting factors to the double-stranded variant surface glycoprotein (VSG) expression site promoter of Trypanosoma brucei. Mol. Biochem. Parasit., 89, 11-23.
44. Ginger,M.L., Blundell,P.A., Lewis,A.M., Browitt,A., Gunzl,A. and Barry,J.D. (2002) Ex vivo and in vitro identification of a consensus promoter for VSG genes expressed by metacyclic-stage trypanosomes in the tsetse fly. Eukaryot. Cell, 1, 1000-1009.
45. van der Werf,A., van Assel,S., Aerts,D., Steinert,M. and Pays,E. (1990) Telomere interactions may condition the programming of antigen expression in Trypanosoma brucei. EMBO J., 9, 1035-1040.
46. Weinstein,B. and Solomon,F. (1990) Phenotypic consequences of tubulin overproduction in Saccharomyces cerevisiae - differences between alpha-tubulin and beta-tubulin. Mol. Cell Biol., 10, 5295-5304.
47. Matthews,K.R., Tschudi,C. and Ullu,E. (1994) A common pyrimidine-rich motif governs transsplicing and polyadenylation of tubulin polycistronic pre-messenger-RNA in trypanosomes. Genes Dev., 8, 491-501.
48. Blattner,J. and Clayton,C.E. (1995) The 3′-untranslated regions from the Trypanosoma brucei phosphoglycerate kinase-encoding genes mediate developmental regulation. Gene, 162, 153-156.
49. Achaz,G., Netter,P. and Coissac,E. (2001) Study of intrachromosomal duplications among the eukaryote genomes. Mol. Biol. Evol., 18, 2280-2288.
50. Achaz,G., Rocha,E.P.C., Netter,P. and Coissac,E. (2002) Origin and fate of repeats in bacteria. Nucleic Acids Res., 30, 2987-2994.
51. Drouin,G. (2002) Characterization of the gene conversions between the multigene family members of the yeast genome. J. Mol. Evol., 55, 14-23.
52. Kruglyak,S., Durrett,R., Schug,M.D. and Aquadro,C.F. (2000) Distribution and abundance of microsatellites in the yeast genome can be explained by a balance between slippage events and point mutations. Mol. Biol. Evol., 17, 1210-1219.
53. Barrett,M.P., MacLeod,A., Tovar,J., Sweetman,J.P., Tait,A., Le Page,R.W.F. and Melville,S.E. (1997) A single locus minisatellite sequence which distinguishes between Trypanosoma brucei isolates. Mol. Biochem. Parasit., 86, 95-99.
54. Pluta,A.F., Mackay,A.M., Ainsztein,A.M., Goldberg,I.G. and Earnshaw,W.C. (1995) Centromere - hub of chromosomal activities. Science, 270, 1591-1594.
55. Su,X.Z., Ferdig,M.T., Huang,Y.M., Huynh,C.Q., Liu,A., You,J.T., Wootton,J.C. and Wellems,T.E. (1999) A genetic map and recombination parameters of the human malaria parasite Plasmodium falciparum. Science, 286, 1351-1353.
56. Henikoff,S. and Henikoff,J.G. (1993) Performance evaluation of amino acid substitution matrices. Proteins, 17, 49-61.