Comparative genome analysis of six malarial parasites using codon usage bias based tools



Manoj Kumar Yadav1 & D Swati2*



1Department of Bioinformatics, MMV, Banaras Hindu University, Varanasi-221005, INDIA; 2Departments of Bioinformatics and Physics, MMV, Banaras Hindu University, Varanasi - 221005, India.


Email; *Corresponding author


Article Type



Received October 31, 2012; Accepted November 05, 2012; Published December 08, 2012



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).



Codon usage bias (CUB), RSCU, tRNA, Optimal codon, Principal Component Analysis (PCA), Effective number of codon (ENC).



CDS: 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.



Yadav & Swati, Bioinformation 8(24): 1230-1239 (2012)

Edited by

P Kangueane






Biomedical Informatics



This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.