Abstract
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.
Highlights
The genome sequence of the protistan parasite Trypanosoma brucei contains many tandem gene arrays
The results reveal the variety of dynamics among tandem arrays and clarify the contribution of concerted evolution and gene conversion in regulating sequence diversity among repetitive genes
After surveying the Trypanosoma brucei genome sequence, 47 tandem arrays with at least four gene copies were identified and characterised. This is unlikely to be an exhaustive list of tandem-duplicated loci in the T. brucei genome since some lengthy tandem arrays may be collapsed to tandem pairs or triplets if gene number could not be resolved during genome assembly
Summary
The genome sequence of the protistan parasite Trypanosoma brucei contains many tandem gene arrays. Evolutionary biology has begun to utilise the abundance of genome sequence data, applying a comparative approach to the evolutionary dynamics of genome structure and sequence [1,2,3]. Within this approach genomic position is a novel source of contextual information, and an additional criterion for assessing homology, independent of gene sequences. The debate has recently concentrated on the relative contributions of evolutionary processes affecting sequence divergence, such as gene conversion, positive and negative selection and concerted evolution, and processes affecting gene quantity and order (page number not for citation purposes). The results reveal the variety of dynamics among tandem arrays and clarify the contribution of concerted evolution and gene conversion in regulating sequence diversity among repetitive genes
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