Dataset Information

The sequence and analysis of Trypanosoma brucei chromosome II.

ABSTRACT: We report here the sequence of chromosome II from Trypanosoma brucei, the causative agent of African sleeping sickness. The 1.2-Mb pairs encode about 470 predicted genes organised in 17 directional clusters on either strand, the largest cluster of which has 92 genes lined up over a 284-kb region. An analysis of the GC skew reveals strand compositional asymmetries that coincide with the distribution of protein-coding genes, suggesting these asymmetries may be the result of transcription-coupled repair on coding versus non-coding strand. A 5-cM genetic map of the chromosome reveals recombinational 'hot' and 'cold' regions, the latter of which is predicted to include the putative centromere. One end of the chromosome consists of a 250-kb region almost exclusively composed of RHS (pseudo)genes that belong to a newly characterised multigene family containing a hot spot of insertion for retroelements. Interspersed with the RHS genes are a few copies of truncated RNA polymerase pseudogenes as well as expression site associated (pseudo)genes (ESAGs) 3 and 4, and 76 bp repeats. These features are reminiscent of a vestigial variant surface glycoprotein (VSG) gene expression site. The other end of the chromosome contains a 30-kb array of VSG genes, the majority of which are pseudogenes, suggesting that this region may be a site for modular de novo construction of VSG gene diversity during transposition/gene conversion events.

SUBMITTER: El-Sayed NM

PROVIDER: S-EPMC169936 | biostudies-literature | 2003 Aug

REPOSITORIES: biostudies-literature

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The sequence and analysis of Trypanosoma brucei chromosome II.

El-Sayed Najib M A NM Ghedin Elodie E Song Jinming J MacLeod Annette A Bringaud Frederic F Larkin Christopher C Wanless David D Peterson Jeremy J Hou Lihua L Taylor Sonya S Tweedie Alison A Biteau Nicolas N Khalak Hanif G HG Lin Xiaoying X Mason Tanya T Hannick Linda L Caler Elisabet E Blandin Gaëlle G Bartholomeu Daniella D Simpson Anjana J AJ Kaul Samir S Zhao Hong H Pai Grace G Van Aken Susan S Utterback Teresa T Haas Brian B Koo Hean L HL Umayam Lowell L Suh Bernard B Gerrard Caroline C Leech Vanessa V Qi Rong R Zhou Shiguo S Schwartz David D Feldblyum Tamara T Salzberg Steven S Tait Andrew A Turner C Michael R CM Ullu Elisabetta E White Owen O Melville Sara S Adams Mark D MD Fraser Claire M CM Donelson John E JE

Nucleic acids research 20030801 16

We report here the sequence of chromosome II from Trypanosoma brucei, the causative agent of African sleeping sickness. The 1.2-Mb pairs encode about 470 predicted genes organised in 17 directional clusters on either strand, the largest cluster of which has 92 genes lined up over a 284-kb region. An analysis of the GC skew reveals strand compositional asymmetries that coincide with the distribution of protein-coding genes, suggesting these asymmetries may be the result of transcription-coupled r ...[more]

PMID: 12907728

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Project description:BackgroundThe genome sequence of the protistan parasite Trypanosoma brucei contains many tandem gene arrays. Gene duplicates are created through tandem duplication and are expressed through polycistronic transcription, suggesting that the primary purpose of long, tandem arrays is to increase gene dosage in an environment where individual gene promoters are absent. This report presents the first account of the tandem gene arrays in the T. brucei genome, employing several related genome sequences to establish how variation is created and removed.ResultsA systematic survey of tandem gene arrays showed that substantial sequence variation existed across the genome; variation from different regions of an array often produced inconsistent phylogenetic affinities. Phylogenetic relationships of gene duplicates were consistent with concerted evolution being a widespread homogenising force. However, tandem duplicates were not usually identical; therefore, any homogenising effect was coincident with divergence among duplicates. Allelic gene conversion was detected using various criteria and was apparently able to both remove and introduce sequence variation. Tandem arrays containing structural heterogeneity demonstrated how sequence homogenisation and differentiation can occur within a single locus.ConclusionThe use of multiple genome sequences in a comparative analysis of tandem gene arrays identified substantial sequence variation among gene duplicates. The distribution of sequence variation is determined by a dynamic balance of conservative and innovative evolutionary forces. Gene trees from various species showed that intraspecific duplicates evolve in concert, perhaps through frequent gene conversion, although this does not prevent sequence divergence, especially where structural heterogeneity physically separates a duplicate from its neighbours. In describing dynamics of sequence variation that have consequences beyond gene dosage, this survey provides a basis for uncovering the hidden functionality within tandem gene arrays in trypanosomatids.

Dataset Information

The sequence and analysis of Trypanosoma brucei chromosome II.

Publications

The sequence and analysis of Trypanosoma brucei chromosome II.

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