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Analysis of codon usage bias of mitochondrial genome in Bombyx mori and its relation to evolution
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  • 作者：Lei Wei (1)
    Jian He (2)
    Xian Jia (1)
    Qi Qi (1)
    Zhisheng Liang (1)
    Hao Zheng (1)
    Yao Ping (1)
    Shuyu Liu (2)
    Jingchen Sun (1)

    1. 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
    2. Guangzhou East Campus Lab Center     ; Sun Yat-sen University ; Guangzhou ; 510006 ; China
  • 关键词：Bombyx mori ; Synonymous codon usage bias ; Genomic DNA ; Mitochondrial DNA ; Evolution
  • 刊名：BMC Evolutionary Biology
  • 出版年：2014
  • 出版时间：December 2014
  • 年：2014
  • 卷：14
  • 期：1
  • 全文大小：919 KB
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  • 刊物主题：Evolutionary Biology; Animal Systematics/Taxonomy/Biogeography; Entomology; Genetics and Population Dynamics; Life Sciences, general;
  • 出版者：BioMed Central
  • ISSN：1471-2148
文摘
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.

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