Analysis of Codon Usage Patterns in <i>Giardia duodenalis</i> Based on Transcriptome Data from <i>Giardia</i>DB

• Main Authors: Xin Li, Xiaocen Wang, Pengtao Gong, Nan Zhang, Xichen Zhang, Jianhua Li
• Format: Article
• Language: English
• Published: MDPI AG 2021-07-01
• Series: Genes
• Subjects: <i>Giardia duodenalis</i>; codon usage bias; transcriptome; optimal codon; evolution
• Online Access: https://www.mdpi.com/2073-4425/12/8/1169

<i>Giardia duodenalis</i>, 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, <i>G. duodenalis</i> CUB remains unclear. Thus, this study analyzes codon usage patterns to assess the restriction factors and obtain useful information in shaping <i>G. duodenalis</i> CUB. The neutrality analysis result indicates that <i>G. duodenalis</i> 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 <i>G. duodenalis</i> genome, ending with G or C. In addition, GC content, gene expression, and protein size also influence <i>G. duodenalis</i> CUB formation. This study systematically analyzes <i>G. duodenalis</i> codon usage pattern and clarifies the mechanisms of <i>G. duodenalis</i> CUB. These results will be very useful to identify new genes, molecular genetic manipulation, and study of <i>G. duodenalis</i> evolution.