Abstract
BackgroundSystematic analyses of sequence features have resulted in a better characterisation of the organisation of the genome. A previous study in prokaryotes on the distribution of sequence repeats, which are notoriously variable and can disrupt the reading frame in genes, showed that these motifs are skewed towards gene termini, specifically the 5' end of genes. For eukaryotes no such intragenic analysis has been performed, though this could indicate the pervasiveness of this distribution bias, thereby helping to expose the selective pressures causing it.ResultsIn fungal gene repertoires we find a similar 5' bias of intragenic mononucleotide repeats, most notably for Candida spp., whereas e.g. Coccidioides spp. display no such bias. With increasing repeat length, ever larger discrepancies are observed in genome repertoire fractions containing such repeats, with up to an 80-fold difference in gene fractions at repeat lengths of 10 bp and longer. This species-specific difference in gene fractions containing large repeats could be attributed to variations in intragenic repeat tolerance. Furthermore, long transcripts experience an even more prominent bias towards the gene termini, with possibly a more adaptive role for repeat-containing short transcripts.ConclusionMononucleotide repeats are intragenically biased in numerous fungal genomes, similar to earlier studies on prokaryotes, indicative of a similar selective pressure in gene organization.
Highlights
Systematic analyses of sequence features have resulted in a better characterisation of the organisation of the genome
Ackermann and Chao postulated that selection for sequence stability in coding regions has been a pervasive force in the distribution biases of mononucleotide repeats (MNRs) in both prokaryotic and eukaryotic
The strongest bias is observed in Candida parapsilosis, where83% (104/125 repeats) of all repeats of 10 bp or longer are in the first quintile of the genes
Summary
Systematic analyses of sequence features have resulted in a better characterisation of the organisation of the genome. A previous study in prokaryotes on the distribution of sequence repeats, which are notoriously variable and can disrupt the reading frame in genes, showed that these motifs are skewed towards gene termini, the 5' end of genes. For eukaryotes no such intragenic analysis has been performed, though this could indicate the pervasiveness of this distribution bias, thereby helping to expose the selective pressures causing it. Ackermann and Chao postulated that selection for sequence stability in coding regions has been a pervasive force in the distribution biases of mononucleotide repeats (MNRs) in both prokaryotic and eukaryotic (page number not for citation purposes)
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