Codon usage bias analyses in three Echinococcus species

MALDONADO, L.; KAMENETZKY, L.; ROSENZVIT, M. C.

Posadas

Congreso; 8th Argentinian Congress of Bioinformatics and Computational Biology (CAB2C); 2017

Species of the genus Echinococcusare Platyhelminthes parasites causatives of hydatid diseases in humans and animalsall over the world. They have complex life cycles comprising an intermediatedand a definitive host. Such hosts infections specificity or preference seems todepend on the Echinococcus species.The study of codon usage in any organism is a powerful tool that can be used toreveal characteristics and evolutive patterns. The codon usage bias is thenon-random usage of synonymous codons for coding amino acids. The synonymoussites are under weak selection, and codon usage bias is kept by the equilibriumin mutational bias, genetic drift and selection pressure. Previously we have obtained the complete genomes of three Echinococcus species  and performed several analyses such as identificationof orthologous genes, quantification of genetic variability  and discovery of microRNA/target interactions.Here, we performed codon usage analyses using a whole genome datasets forcomparative genome analysis of E.canadensis, E. multilocularis andE. granulosus by applying codonW,CodonO softwares and principal component analysis (PCA) on 3000-4000 genes. Thenucleotide content in each position of the codons was used as a measure ofevolution effectors.As demonstrated by PCA and ENc analyses many genes have non-randomselection of codons. Indeed genes with strong codon bias seem to be expressedat a higher level compared to other genes. However, most of the genes appearnot to have a biased codon usage and the frequencies of codons among the Echinococcus species exhibits a strongRSCU correlation among each other. On the other hand the use of UAG as a stopcodon signal is absent for all the genesComparative analysis of codon usage among the Ehinococcus species could reveal genes responsible forspecie-specific phenotypes and host preference infections. The differentialcodon usage choices are also relevant to human infecting by many pathogensorganisms.