Analysis of codon usage bias of mitochondrial genome in Bombyx mori and its relation to evolution

BMC Evolutionary Biology

Jingchen Sun²  Shuyu Liu¹  Yao Ping²  Hao Zheng²  Zhisheng Liang²  Qi Qi²  Xian Jia²  Jian He¹  Lei Wei² 

[1] Guangzhou East Campus Lab Center, Sun Yat-sen University, Guangzhou 510006, China;Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China

关键词: Evolution;    Mitochondrial DNA;    Genomic DNA;    Synonymous codon usage bias;    Bombyx mori;   

Others  :  1121751
DOI  :  10.1186/s12862-014-0262-4

 received in 2014-08-20, accepted in 2014-12-09,  发布年份 2014

【 摘 要 】

Background

Synonymous codon usage bias (SCUB) is an inevitable phenomenon in organismic taxa, generally referring to differences in the occurrence frequency of codons across different species or within the genome of the same species. SCUB happens in various degrees under pressure from nature selection, mutation bias and other factors in different ways. It also attaches great significance to gene expression and species evolution, however, a systematic investigation towards the codon usage in Bombyx mori (B. mori) has not been reported yet. Moreover, it is still indistinct about the reasons contributing to the bias or the relationship between the bias and the evolution of B. mori.

Results

The comparison of the codon usage pattern between the genomic DNA (gDNA) and the mitochondrial DNA (mtDNA) from B. mori suggests that mtDNA has a higher level of codon bias. Furthermore, the correspondence analysis suggests that natural selection, such as gene length, gene function and translational selection, dominates the codon preference of mtDNA, while the composition constraints for mutation bias only plays a minor role. Additionally, the clustering results of the silkworm superfamily suggest a lack of explicitness in the relationship between the codon usage of mitogenome and species evolution.

Conclusions

Among the complicated influence factors leading to codon bias, natural selection is found to play a major role in shaping the high bias in the mtDNA of B. mori from our current data. Although the cluster analysis reveals that codon bias correlates little with the species evolution, furthermore, a detailed analysis of codon usage of mitogenome provides better insight into the evolutionary relationships in Lepidoptera. However, more new methods and data are needed to investigate the relationship between the mtDNA bias and evolution.

【 授权许可】

   
2014 Wei et al.; licensee BioMed Central Ltd.

【 图 表 】

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