Comparative Genomics of Trypanosomatid Pathogens using Codon Usage Bias |
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Authors: | Mayank Rashmi D Swati |
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Institution: | 1.Department of Bioinformatics, MMV, Banaras Hindu University, Varanasi-221005, India;2.Department of Physics, MMV, Banaras Hindu University, Varanasi 221005, India |
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Abstract: | It is well known that an amino acid can be encoded by more than one codon, called synonymous codons. The preferential use of
one particular codon for coding an amino acid is referred to as codon usage bias (CUB). A quantitative analytical method, CUB and
a related tool, Codon Adaptative Index have been applied to comparatively study whole genomes of a few pathogenic
Trypanosomatid species. This quantitative attempt is of direct help in the comparison of qualitative features like mutational and
translational selection. Pathogens of the Leishmania and Trypanosoma genus cause debilitating disease and suffering in human
beings and animals. Of these, whole genome sequences are available for only five species. The complete coding sequences (CDS),
highly expressed, essential and low expressed genes have all been studied for their CUB signature. The codon usage bias of
essential genes and highly expressed genes show distribution similar to codon usage bias of all CDSs in Trypanosomatids.
Translational selection is the dominant force selecting the preferred codon, and selection due to mutation is negligible. In contrast
to an earlier study done on these pathogens, it is found in this work that CUB and CAI may be used to distinguish the
Trypanosomatid genomes at the sub-genus level. Further, CUB may effectively be used as a signature of the species differentiation
by using Principal Component Analysis (PCA).AbbreviationsCUB - Codon Usage Bias,
CAI - Codon Adaptative Index,
CDS - Coding sequences,
t-RNA - Transfer RNA,
PCA - Principal Component Analysis. |
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Keywords: | Codon Usage Bias Codon Adaptation Index Essential genes Highly expressed genes Translational selection t-RNA |
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