Expression levels and codon usage patterns in nuclear genes of the filarial nematodeWucheraria bancroftiand the blood flukeSchistosoma haematobium

Abstract

Synonymous codons are used with different frequencies, a phenomenon known as codon bias, which exists in many genomes and is mainly resolute by mutation and selection. To elucidate the genetic characteristics and evolutionary relationship of Wucheraria bancrofti and Schistosoma haematobium we examined the pattern of synonymous codon usage in nuclear genes of both the species. The mean overall GC contents of W. bancrofti and S. haematobium were 43.41 and 36.37%, respectively, which suggests that genes in both the species were AT rich. The value of the High Effective Number of Codons in both species suggests that codon usage bias was weak. Both species had a wide range of P3 distribution in the neutrality plot, with a significant correlation between P12 and P3. The codons were closer to the axes in correspondence analysis, suggesting that mutation pressure influenced the codon usage pattern in these species. We have identified the more frequently used codons in these species, most codons ending with an A or T. The nucleotides A/T and C/G were not proportionally used at the third position of codons, which reveals that natural selection might influence the codon usage patterns. The regression equation of P12 on P3 suggests that natural selection might have played a major role, while mutational pressure played a minor role in codon usage pattern in both species. These results form the basis of exploring the evolutionary mechanisms and the heterologous expression of medically important proteins of W. bancrofti and S. haematobium.

Compositional Analysis of Flatworm Genomes Shows Strong Codon Usage Biases Across All Classes

“…as preponderant forces. More recently, studies on S. haematobium and S. japonicum confirmed a major role of natural selection in shaping the codon usage bias in these species (Mazumder et al, 2017a; Mazumder et al, 2017b). Several studies analyzed codon usage on the available genomes and transcriptomes of Taenidae species showing weak codon bias and a higher GC3 in highly expressed genes explained by combined mutational and selection forces (Chen et al, 2013; Yang et al, 2014; Yang et al, 2015; Huang et al, 2017).…”

“…Besides the effect at synonymous codon usage, it has been shown that strong GC bias could lead to changes in amino acid frequencies (Behura and Severson, 2013; Li et al, 2015). While this has not been explored widely in flatworms, several advances have been made in nematodes (Cutter et al, 2006; Mitreva et al, 2006; Mazumder et al, 2017a; Mazumder et al, 2017b). It is not clear yet how genomic GC differences could be influencing the codon usage and amino acid composition of proteins in Platyhelminthes and if these variations correlate with the ecological and physiological diversity in the phylum.…”

Codon Usage Bias Correlates With Gene Length in Neurodegeneration Associated Genes

“…A comparison of the AT and GC skews in 30 avian mitochondrial genomes revealed that parrots have unusually strong compositional asymmetry (AT-and GC-skew) in their coding sequences (Eberhard and Wright, 2016). In W. bancrofti and S. haematobium, the GC, AT, purine, pyrimidine, amino, and keto skews were negatively associated with CUB, except for the pyrimidine skew in S. haematobium (Mazumder et al, 2017). Contrarily, in amphibians Bombina bombina, B. fortinuptialis, B. lichuanensis, B. maxima, B. microdeladigitora, B. orientalis, and B. variegate, no skew was correlated to CUB (Barbhuiya et al, 2019).…”

“…A significant correlation between the effective number of codons (ENC) and different skews (GC, AT, purine, pyrimidine, amino, and keto skews) has also been reported in Wuchereria bancrofti and Schistosoma haematobium , wherein all the skews were negative in both the organisms, except for that of pyrimidine in S. haematobium . This suggests a significant role of CUB on nucleotide disproportion ( Mazumder et al, 2017 ); however, the different skews represent a marker for a specific genus and species.…”