Codon Usage Bias and Determining Forces in Taenia Solium Genome

Overview

Journal Korean J Parasitol

Specialty Parasitology

Date 2016 Jan 23

PMID 26797435

Citations 8

Authors

Xing Yang

Xusheng Ma

Xuenong Luo

Houjun Ling

Xichen Zhang

Xuepeng Cai

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

Comparative analysis of codon usage patterns and phylogenetic implications of five mitochondrial genomes of the genus Ishihara, 1955 (Hemiptera, Cicadellidae, Megophthalminae).

Li M, Wang J, Dai R, Smagghe G, Wang X, You S PeerJ. 2023; 11:e16058.

PMID: 37780390 PMC: 10538298. DOI: 10.7717/peerj.16058.

Evolution of codon usage in genomes and its impact on the host.

Rahman S, Rehman H, Rahman I, Khan M, Rahim F, Ali H Front Vet Sci. 2023; 9:1021440.

PMID: 36713873 PMC: 9875090. DOI: 10.3389/fvets.2022.1021440.

Analysis of codon usage bias of lumpy skin disease virus causing livestock infection.

Rahman S, Rehman H, Rahman I, Rauf A, Alshammari A, Alharbi M Front Vet Sci. 2022; 9:1071097.

PMID: 36544551 PMC: 9762553. DOI: 10.3389/fvets.2022.1071097.

Codon Usage is Influenced by Compositional Constraints in Genes Associated with Dementia.

Alqahtani T, Khandia R, Puranik N, Alqahtani A, Alghazwani Y, Alshehri S Front Genet. 2022; 13:884348.

PMID: 36017501 PMC: 9395603. DOI: 10.3389/fgene.2022.884348.

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

Lamolle G, Fontenla S, Rijo G, Tort J, Smircich P Front Genet. 2019; 10:771.

PMID: 31543897 PMC: 6739440. DOI: 10.3389/fgene.2019.00771.

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