Abstract
Codon usage bias (CUB) is an omnipresent phenomenon, which occurs in nearly all organisms. Previous studies of codon bias in Plasmodium species were based on a limited dataset. This study uses whole genome datasets for comparative genome analysis of six Plasmodium species using CUB and other related methods for the first time. Codon usage bias, compositional variation in translated amino acid frequency, effective number of codons and optimal codons are analyzed for P.falciparum, P.vivax, P.knowlesi, P.berghei, P.chabaudii and P.yoelli. A plot of effective number of codons versus GC3 shows their differential codon usage pattern arises due to a combination of mutational and translational selection pressure. The increased relative usage of adenine and thymine ending optimal codons in highly expressed genes of P.falciparum is the result of higher composition biased pressure, and usage of guanine and cytosine bases at third codon position can be explained by translational selection pressure acting on them. While higher usage of adenine and thymine bases at third codon position in optimal codons of P.vivax highlights the role of translational selection pressure apart from composition biased mutation pressure in shaping their codon usage pattern. The frequency of those amino acids that are encoded by AT ending codons are significantly high in P.falciparum due to action of high composition biased mutational pressure compared with other Plasmodium species. The CUB variation in the three rodent parasites, P.berghei, P.chabaudii and P.yoelli is strikingly similar to that of P.falciparum. The simian and human malarial parasite, P.knowlesi shows a variation in codon usage bias similar to P.vivax but on closer study there are differences confirmed by the method of Principal Component Analysis (PCA).AbbreviationsCDS - Coding sequences, GC1 - GC composition at first site of codon, GC2 - GC composition at second site of codon, GC3 - GC composition at third site of codon, Ala - Alanine, Arg - Arginine, Asn - Asparagine, Asp - Aspartic acid, Cys - Cysteine, Gln - Glutamine Glu - Glutamic acid Gly - Glycine His - Histidine Ile - Isoleucine Leu - Leucine Lys - Lysine Met - Methionine Phe - Phenylalanine Pro - Proline Ser - Serine Thr - Threonine Trp - Tryptophan Tyr - Tyrosine Val - Valine.
Highlights
Codon usage bias (CUB) is an omnipresent phenomenon, which occurs in most organisms
First - whether the codon usage pattern in Plasmodium genus is conserved or not; second - is the comparative analysis of six different Plasmodium species to understand their phylogenetic relationships possible on the basis of codon usage bias and third-to identify the role of mutational and translational selection forces using their genome sequence data for shaping codon usage pattern
Relative synonymous codon usage (RSCU) RSCU value of each codon is the observed frequency of that codon divided by the expected frequency for synonymous codons of an amino acid using equal usage as a conjecture
Summary
Codon usage bias (CUB) is an omnipresent phenomenon, which occurs in most organisms. While higher usage of adenine and thymine bases at third codon position in optimal codons of P.vivax highlights the role of translational selection pressure apart from composition biased mutation pressure in shaping their codon usage pattern The frequency of those amino acids that are encoded by AT ending codons are significantly high in P.falciparum due to action of high composition biased mutational pressure compared with other Plasmodium species. The intra-genomic and inter-genomic codon usage variability is mainly governed by various biological factors simultaneously but directional mutational pressure on DNA sequences and translational selection forces are the key role players [15] Previous investigations on these parasites and their vectors [16] showed differences in their genomic architecture as well as ecological habitat. First - whether the codon usage pattern in Plasmodium genus is conserved or not; second - is the comparative analysis of six different Plasmodium species to understand their phylogenetic relationships possible on the basis of codon usage bias and third-to identify the role of mutational and translational selection forces using their genome sequence data for shaping codon usage pattern
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