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Nucleic Acids Research, 2003, Vol. 31, No. 16 4864-4873
© 2003 Oxford University Press

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

Neil Hall, Matthew Berriman, Nicola J. Lennard, Barbara R. Harris, Christiane Hertz-Fowler, Emmanuelle N. Bart-Delabesse1, Caroline S. Gerrard1, Rebecca J. Atkin, Andrew J. Barron, Sharen Bowman, Sarah P. Bray-Allen, Frédéric Bringaud2, Louise N. Clark, Craig H. Corton, Ann Cronin, Robert Davies, Jonathon Doggett, Audrey Fraser, Eric Grüter1, Sarah Hall, A. David Harper, Mike P. Kay, Vanessa Leech1, Rebecca Mayes, Claire Price, Michael A. Quail, Ester Rabbinowitsch, Christopher Reitter1, Kim Rutherford, Jürgen Sasse1, Sarah Sharp, Ratna Shownkeen, Annette MacLeod3, Sonya Taylor4, Alison Tweedie3, C. Michael R. Turner4, Andrew Tait3, Keith Gull5, Bart Barrell and Sara E. Melville*,1

The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK, 1 University of Cambridge Department of Pathology, Tennis Court Road, Cambridge CB2 1QP, UK, 2 Université Victor Segalen Bordeaux II, Rue Léo Saignat 33076 Bordeaux, France, 3 Wellcome Centre for Molecular Parasitology, University of Glasgow, 56 Dumbarton Road, Glasgow G11 6NU, UK, 4 Division of Infection and Immunity, Joseph Black Building, Institute of Biological and Life Science, Glasgow G12 8QQ, UK and 5 Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK

*To whom correspondence should be addressed. Tel: +44 1223 765668; Fax: +44 1223 333737; Email: sm160{at}cam.ac.uk
Present address:
Sharen Bowman, Syngenta, Jealott’s Hill International Research Centre Bracknell, Berkshire RG42 6EY, UK
+AL929608, AJ507434–43, AJ512347–69

The African trypanosome, Trypanosoma brucei, causes sleeping sickness in humans in sub-Saharan Africa. Here we report the sequence and analysis of the 1.1 Mb chromosome I, which encodes approximately 400 predicted genes organised into directional clusters, of which more than 100 are located in the largest cluster of 250 kb. A 160-kb region consists primarily of three gene families of unknown function, one of which contains a hotspot for retroelement insertion. We also identify five novel gene families. Indeed, almost 20% of predicted genes are members of families. In some cases, tandemly arrayed genes are 99–100% identical, suggesting an active process of amplification and gene conversion. One end of the chromosome consists of a putative bloodstream-form variant surface glycoprotein (VSG) gene expression site that appears truncated and degenerate. The other chromosome end carries VSG and expression site-associated genes and pseudogenes over 50 kb of subtelomeric sequence where, unusually, the telomere-proximal VSG gene is oriented away from the telomere. Our analysis includes the cataloguing of minor genetic variations between the chromosome I homologues and an estimate of crossing-over frequency during genetic exchange. Genetic polymorphisms are exceptionally rare in sequences located within and around the strand-switches between several gene clusters.


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