Abstract
Giardia duodenalis, a flagellated parasitic protozoan, the most common cause of parasite-induced diarrheal diseases worldwide. Codon usage bias (CUB) is an important evolutionary character in most species. However, G. duodenalis CUB remains unclear. Thus, this study analyzes codon usage patterns to assess the restriction factors and obtain useful information in shaping G. duodenalis CUB. The neutrality analysis result indicates that G. duodenalis has a wide GC3 distribution, which significantly correlates with GC12. ENC-plot result—suggesting that most genes were close to the expected curve with only a few strayed away points. This indicates that mutational pressure and natural selection played an important role in the development of CUB. The Parity Rule 2 plot (PR2) result demonstrates that the usage of GC and AT was out of proportion. Interestingly, we identified 26 optimal codons in the G. duodenalis genome, ending with G or C. In addition, GC content, gene expression, and protein size also influence G. duodenalis CUB formation. This study systematically analyzes G. duodenalis codon usage pattern and clarifies the mechanisms of G. duodenalis CUB. These results will be very useful to identify new genes, molecular genetic manipulation, and study of G. duodenalis evolution.
Highlights
Codon usage bias is a widespread feature among both prokaryotes and eukaryotes, which describes synonymous codons that are not used at the same frequency in the process of gene translation [1,2,3]
The results suggested that the GC content of 5968 G. duodenalis genes exhibited a distinctly unimodal distribution
The GC contents of G. duodenalis genes varied from 39.1% to 81.1% (SD = 0.0523), and the GC contents of the 5968 coding sequences (CDS) were mainly ranged from 45% to 55%
Summary
Codon usage bias is a widespread feature among both prokaryotes and eukaryotes, which describes synonymous codons that are not used at the same frequency in the process of gene translation [1,2,3]. CUB is widely distributed and affected by tRNA abundance [4], nucleotide composition [5], translational processes [6], gene function [7,8], protein structure [9], hydrophobicity [10], environment temperature [11], etc. Analysis of synonymous codon usage bias has various important applications, such as degenerate primer design [14], heterologous gene expression [15], species origin determination [16], the prediction of the expression level of genes [17,18], and the prediction of gene functions [19]. Previous studies of G. duodenalis codon usage only analyzed with small number of genes [33,34]
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