title: Analysis of codon usage bias of mitochondrial genome in Bombyx mori and its relation to evolution.
abstract: 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.
authors.affiliation: 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. 404770794@qq.com.
authors.forename: Lei
authors.initials: L
authors.lastname: Wei
authors.affiliation: Guangzhou East Campus Lab Center, Sun Yat-sen University, Guangzhou, 510006, China. hejian22@mail.sysu.edu.cn.
authors.forename: Jian
authors.initials: J
authors.lastname: He
authors.affiliation: 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. tomjim100@sina.com.
authors.forename: Xian
authors.initials: X
authors.lastname: Jia
authors.affiliation: 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. 412872021@qq.com.
authors.forename: Qi
authors.initials: Q
authors.lastname: Qi
authors.affiliation: 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. 185605779@qq.com.
authors.forename: Zhisheng
authors.initials: Z
authors.lastname: Liang
authors.affiliation: 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. 774926329@qq.com.
authors.forename: Hao
authors.initials: H
authors.lastname: Zheng
authors.affiliation: 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. 513206918@qq.com.
authors.forename: Yao
authors.initials: Y
authors.lastname: Ping
authors.affiliation: Guangzhou East Campus Lab Center, Sun Yat-sen University, Guangzhou, 510006, China. lsy@mail.sysu.edu.cn.
authors.forename: Shuyu
authors.initials: S
authors.lastname: Liu
authors.affiliation: 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. cyfz@scau.edu.cn.
authors.forename: Jingchen
authors.initials: J
authors.lastname: Sun
mesh_terms: D000818:Animals; D005075:Biological Evolution; D012831:Bombyx / Q000166:cytology / Q000235:genetics*; D003062:Codon; D019143:Evolution, Molecular; D054629:Genome, Mitochondrial; D009154:Mutation; D010802:Phylogeny; D012641:Selection, Genetic
chemical_list: D003062:Codon