Parasites, Hosts and Diseases

"codon usage"

Original Articles

Codon Usage Patterns of Tyrosinase Genes in Clonorchis sinensis: Young-An Bae; Korean J Parasitol 2017;55(2):175-183.
Published online April 30, 2017; DOI: https://doi.org/10.3347/kjp.2017.55.2.175

Abstract
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Codon usage bias (CUB) is a unique property of genomes and has contributed to the better understanding of the molecular features and the evolution processes of particular gene. In this study, genetic indices associated with CUB, including relative synonymous codon usage and effective numbers of codons, as well as the nucleotide composition, were investigated in the Clonorchis sinensis tyrosinase genes and their platyhelminth orthologs, which play an important role in the eggshell formation. The relative synonymous codon usage patterns substantially differed among tyrosinase genes examined. In a neutrality analysis, the correlation between GC₁₂ and GC₃ was statistically significant, and the regression line had a relatively gradual slope (0.218). NC-plot, i.e., GC₃ vs effective number of codons (ENC), showed that most of the tyrosinase genes were below the expected curve. The codon adaptation index (CAI) values of the platyhelminth tyrosinases had a narrow distribution between 0.685/0.714 and 0.797/0.837, and were negatively correlated with their ENC. Taken together, these results suggested that CUB in the tyrosinase genes seemed to be basically governed by selection pressures rather than mutational bias, although the latter factor provided an additional force in shaping CUB of the C. sinensis and Opisthorchis viverrini genes. It was also apparent that the equilibrium point between selection pressure and mutational bias is much more inclined to selection pressure in highly expressed C. sinensis genes, than in poorly expressed genes.

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Analysis of codon usage bias in mitochondrial CO gene among platyhelminthes
Gulshana A. Mazumder, Arif Uddin, Supriyo Chakraborty
Molecular and Biochemical Parasitology.2021; 245: 111410. CrossRef

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136 Download
1 Web of Science
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Codon Usage Bias and Determining Forces in Taenia solium Genome: Xing Yang, Xusheng Ma, Xuenong Luo, Houjun Ling, Xichen Zhang, Xuepeng Cai; Korean J Parasitol 2015;53(6):689-697.
Published online December 31, 2015; DOI: https://doi.org/10.3347/kjp.2015.53.6.689

Abstract
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The tapeworm Taenia solium is an important human zoonotic parasite that causes great economic loss and also endangers public health. At present, an effective vaccine that will prevent infection and chemotherapy without any side effect remains to be developed. In this study, codon usage patterns in the T. solium genome were examined through 8,484 protein-coding genes. Neutrality analysis showed that T. solium had a narrow GC distribution, and a significant correlation was observed between GC12 and GC3. Examination of an NC (ENC vs GC3s)-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENC (the effective number of codons) values were detected below the expected curve, suggesting that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally. We also identified 26 optimal codons in the T. solium genome, all of which ended with either a G or C residue. These optimal codons in the T. solium genome are likely consistent with tRNAs that are highly expressed in the cell, suggesting that mutational and translational selection forces are probably driving factors of codon usage bias in the T. solium genome.

Citations

Citations to this article as recorded by

Distinct codon usage signatures reflecting evolutionary and pathogenic adaptation in the Acinetobacter baumannii complex
Ujwal Dahal, Anuj Sharma, Karan Paul, Anu Bansal, Shelly Gupta
European Journal of Clinical Microbiology & Infectious Diseases.2025; 44(11): 2803. CrossRef
Evolution of codon usage in Taenia saginata genomes and its impact on the host
Siddiq Ur Rahman, Hassan Ur Rehman, Inayat Ur Rahman, Muazzam Ali Khan, Fazli Rahim, Hamid Ali, Dekun Chen, Wentao Ma
Frontiers in Veterinary Science.2023;[Epub] CrossRef
Comparative analysis of codon usage patterns and phylogenetic implications of five mitochondrial genomes of the genus Japanagallia Ishihara, 1955 (Hemiptera, Cicadellidae, Megophthalminae)
Min Li, Jiajia Wang, Renhuai Dai, Guy Smagghe, Xianyi Wang, Siying You
PeerJ.2023; 11: e16058. CrossRef
Codon Usage is Influenced by Compositional Constraints in Genes Associated with Dementia
Taha Alqahtani, Rekha Khandia, Nidhi Puranik, Ali M. Alqahtani, Yahia Alghazwani, Saad Ali Alshehri, Kumarappan Chidambaram, Mohammad Amjad Kamal
Frontiers in Genetics.2022;[Epub] CrossRef
Analysis of codon usage bias of lumpy skin disease virus causing livestock infection
Siddiq Ur Rahman, Hassan Ur Rehman, Inayat Ur Rahman, Abdur Rauf, Abdulrahman Alshammari, Metab Alharbi, Noor ul Haq, Hafiz Ansar Rasul Suleria, Sayed Haidar Abbas Raza
Frontiers in Veterinary Science.2022;[Epub] CrossRef
Codon usage pattern in Gnetales evolved in close accordance with the Gnetifer hypothesis
Aasim Majeed, Harpreet Kaur, Amitozdeep Kaur, Sreemoyee Das, Josepheena Joseph, Pankaj Bhardwaj
Botanical Journal of the Linnean Society.2021; 196(4): 423. CrossRef
Analysis of codon usage bias in mitochondrial CO gene among platyhelminthes
Gulshana A. Mazumder, Arif Uddin, Supriyo Chakraborty
Molecular and Biochemical Parasitology.2021; 245: 111410. CrossRef
Genetic evolution and codon usage analysis of NKX-2.5 gene governing heart development in some mammals
Arup Kr. Malakar, Binata Halder, Prosenjit Paul, Himangshu Deka, Supriyo Chakraborty
Genomics.2020; 112(2): 1319. CrossRef
Selection constraints determine preference for A/U-ending codons in Taxus contorta
Aasim Majeed, Harpreet Kaur, Pankaj Bhardwaj
Genome.2020; 63(4): 215. CrossRef
Analysis of codon usage pattern of mitochondrial ND genes in Platyhelminthes
Gulshana A. Mazumder, Arif Uddin, Supriyo Chakraborty
Molecular and Biochemical Parasitology.2020; 238: 111294. CrossRef
Compositional Analysis of Flatworm Genomes Shows Strong Codon Usage Biases Across All Classes
Guillermo Lamolle, Santiago Fontenla, Gastón Rijo, Jose F. Tort, Pablo Smircich
Frontiers in Genetics.2019;[Epub] CrossRef
Compositional bias coupled with selection and mutation pressure drives codon usage in Brassica campestris genes
Prosenjit Paul, Arup Kumar Malakar, Supriyo Chakraborty
Food Science and Biotechnology.2018; 27(3): 725. CrossRef
Whole genome analysis of codon usage in Echinococcus
Lucas L. Maldonado, Georgina Stegmayer, Diego H. Milone, Guilherme Oliveira, Mara Rosenzvit, Laura Kamenetzky
Molecular and Biochemical Parasitology.2018; 225: 54. CrossRef
Comprehensive Analysis of Codon Usage on Rabies Virus and Other Lyssaviruses
Xu Zhang, Yuchen Cai, Xiaofeng Zhai, Jie Liu, Wen Zhao, Senlin Ji, Shuo Su, Jiyong Zhou
International Journal of Molecular Sciences.2018; 19(8): 2397. CrossRef
Codon Usage Patterns of Tyrosinase Genes in Clonorchis sinensis
Young-An Bae
The Korean Journal of Parasitology.2017; 55(2): 175. CrossRef

12,477 View
130 Download
15 Web of Science
Crossref

Codon usage and bias in mitochondrial genomes of parasitic platyhelminthes: Thanh Hoa Le, Donald Peter McManus, David Blair; Korean J Parasitol 2004;42(4):159-167.
Published online December 20, 2004; DOI: https://doi.org/10.3347/kjp.2004.42.4.159

Abstract
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Sequences of the complete protein-coding portions of the mitochondrial (mt) genome were analysed for 6 species of cestodes (including hydatid tapeworms and the pork tapeworm) and 5 species of trematodes (blood flukes and liver- and lung-flukes). A near-complete sequence was also available for an additional trematode (the blood flukeSchistosoma malayensis). All of these parasites belong to a large flatworm taxon named the Neodermata. Considerable variation was found in the base composition of the protein-coding genes among these neodermatans. This variation was reflected in statistically-significant differences in numbers of each inferred amino acid between many pairs of species. Both convergence and divergence in nucleotide, and hence amino acid, composition was noted among groups within the Neodermata. Considerable variation in skew (unequal representation of complementary bases on the same strand) was found among the species studied. A pattern is thus emerging of diversity in the mt genome in neodermatans that may cast light on evolution of mt genomes generally.

Citations

Citations to this article as recorded by

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Evolution of codon usage in Taenia saginata genomes and its impact on the host
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Frontiers in Veterinary Science.2023;[Epub] CrossRef
Characterization of the complete mitochondrial genome of the fluke of turdus, Plagiorchis elegans, and phylogenetic implications
Rong Li, Hui-Mei Wang, Guo-Hua Liu, Ya Tu, Yuan-Ping Deng
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Analysis of codon usage bias of lumpy skin disease virus causing livestock infection
Siddiq Ur Rahman, Hassan Ur Rehman, Inayat Ur Rahman, Abdur Rauf, Abdulrahman Alshammari, Metab Alharbi, Noor ul Haq, Hafiz Ansar Rasul Suleria, Sayed Haidar Abbas Raza
Frontiers in Veterinary Science.2022;[Epub] CrossRef
Understanding the codon usage patterns of mitochondrial CO genes among Amphibians
Parvin A. Barbhuiya, Arif Uddin, Supriyo Chakraborty
Gene.2021; 777: 145462. CrossRef
Characterization of the complete mitochondrial genome of Diplostomum baeri
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The complete mitochondrial genome of Paragonimus ohirai (Paragonimidae: Trematoda: Platyhelminthes) and its comparison with P. westermani congeners and other trematodes
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Compositional Analysis of Flatworm Genomes Shows Strong Codon Usage Biases Across All Classes
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Compositional bias coupled with selection and mutation pressure drives codon usage in Brassica campestris genes
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Phenotypic plasticity of six unusual cercariae in nassariid gastropods and their relationships to the Acanthocolpidae and Brachycladiidae (Digenea)
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