Analysis of codon usage pattern in Taenia saginata based on a transcriptome dataset

Particle and Fibre Toxicology

Xuepeng Cai¹  Xuenong Luo²  Xing Yang¹ 

[1] College of Veterinary Medicine, Jilin University, Changchun 130000, PR China;State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, PR China

关键词: Optimal codon;    Trancriptome;    Codon usage bias;    Taenia saginata;   

Others  :  1148913
DOI  :  10.1186/s13071-014-0527-1

 received in 2014-04-11, accepted in 2014-11-06,  发布年份 2014

【 摘 要 】

Background

Codon usage bias is an important evolutionary feature in a genome and has been widely documented in many genomes. Analysis of codon usage bias has significance for mRNA translation, design of transgenes, new gene discovery, and studies of molecular biology and evolution, etc. However, the information about synonymous codon usage pattern of T. saginata genome remains unclear. T. saginata is a food-borne zoonotic cestode which infects approximataely 50 million humans worldwide, and causes significant health problems to the host and considerable socio-economic losses as a consequence. In this study, synonymous codon usage in T. saginata were examined.

Methods

Total RNA was isolated from T. saginata cysticerci and 91,487 unigenes were generated using Illumina sequencing technology. After filtering, the final sequence collection containing 11,399 CDSs was used for our analysis.

Results

Neutrality analysis showed that the T. saginata had a wide GC3 distribution and a significant correlation was observed between GC12 and GC3. NC-plot showed most of genes on or close to the expected curve, but only a few points with low-ENC values were below it, 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 twenty-three optimal codons in the T. saginata genome, all of which were ended with a G or C residue. These results suggest that mutational and selection forces are probably driving factors of codon usage bias in T. saginata genome. Meanwhile, other factors such as protein length, gene expression, GC content of genes, the hydropathicity of each protein also influence codon usage.

Conclusions

Here, we systematically analyzed the codon usage pattern and identified factors shaping in codon usage bias in T. saginata. Currently, no complete nuclear genome is available for codon usage analysis at the genome level in T. saginata. This is the first report to investigate codon biology in T. sagninata. Such information does not only bring about a new perspective for understanding the mechanisms of biased usage of synonymous codons but also provide useful clues for molecular genetic engineering and evolutionary studies.

【 授权许可】

   
2014 Yang et al.; licensee BioMed Central.

【 图 表 】

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