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Open Access Research article

Codon-triplet context unveils unique features of the Candida albicans protein coding genome

Gabriela R Moura1, José P Lousado2, Miguel Pinheiro3, Laura Carreto1, Raquel M Silva1, José L Oliveira3 and Manuel AS Santos1*

Author Affiliations

1 Department of Biology and CESAM. University of Aveiro, 3810-193 Aveiro, Portugal

2 ESTGL, Polytechnic Institute of Viseu, 5100-074 Lamego, Portugal

3 Institute of Electronics and Telematics Engineering (IEETA). University of Aveiro, 3810-193 Aveiro, Portugal

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BMC Genomics 2007, 8:444  doi:10.1186/1471-2164-8-444

Published: 29 November 2007

Abstract

Background

The evolutionary forces that determine the arrangement of synonymous codons within open reading frames and fine tune mRNA translation efficiency are not yet understood. In order to tackle this question we have carried out a large scale study of codon-triplet contexts in 11 fungal species to unravel associations or relationships between codons present at the ribosome A-, P- and E-sites during each decoding cycle.

Results

Our analysis unveiled high bias within the context of codon-triplets, in particular strong preference for triplets of identical codons. We have also identified a surprisingly large number of codon-triplet combinations that vanished from fungal ORFeomes. Candida albicans exacerbated these features, showed an unbalanced tRNA population for decoding its pool of codons and used near-cognate decoding for a large set of codons, suggesting that unique evolutionary forces shaped the evolution of its ORFeome.

Conclusion

We have developed bioinformatics tools for large-scale analysis of codon-triplet contexts. These algorithms identified codon-triplets context biases, allowed for large scale comparative codon-triplet analysis, and identified rules governing codon-triplet context. They could also detect alterations to the standard genetic code.