title: Non-uniqueness of factors constraint on the codon usage in Bombyx mori.
abstract: BACKGROUND
  The analysis of codon usage is a good way to understand the genetic and evolutionary characteristics of an organism. However, there are only a few reports related with the codon usage of the domesticated silkworm, Bombyx mori (B. mori). Hence, the codon usage of B. mori was analyzed here to reveal the constraint factors and it could be helpful to improve the bioreactor based on B. mori.
  
  
  RESULTS
  A total of 1,097 annotated mRNA sequences from B. mori were analyzed, revealing there is only a weak codon bias. It also shows that the gene expression level is related to the GC content, and the amino acids with higher general average hydropathicity (GRAVY) and aromaticity (Aromo). And the genes on the primary axis are strongly positively correlated with the GC content, and GC3s. Meanwhile, the effective number of codons (ENc) is strongly correlated with codon adaptation index (CAI), gene length, and Aromo values. However, the ENc values are correlated with the second axis, which indicates that the codon usage in B. mori is affected by not only mutation pressure and natural selection, but also nucleotide composition and the gene expression level. It is also associated with Aromo values, and gene length. Additionally, B. mori has a greater relative discrepancy in codon preferences with Drosophila melanogaster (D. melanogaster) or Saccharomyces cerevisiae (S. cerevisiae) than with Arabidopsis thaliana (A. thaliana), Escherichia coli (E. coli), or Caenorhabditis elegans (C. elegans).
  
  
  CONCLUSIONS
  The codon usage bias in B. mori is relatively weak, and many influence factors are found here, such as nucleotide composition, mutation pressure, natural selection, and expression level. Additionally, it is also associated with Aromo values, and gene length. Among them, natural selection might play a major role. Moreover, the "optimal codons" of B. mori are all encoded by G and C, which provides useful information for enhancing the gene expression in B. mori through codon optimization.
authors.affiliation: Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, and Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Centre, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China. tomjim100@sina.com.
authors.forename: Xian
authors.initials: X
authors.lastname: Jia
authors.affiliation: Guangzhou East Campus Lab Centre, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China. lsy@mail.sysu.edu.cn.
authors.forename: Shuyu
authors.initials: S
authors.lastname: Liu
authors.affiliation: Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, and Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Centre, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China. 774926329@qq.com.
authors.forename: Hao
authors.initials: H
authors.lastname: Zheng
authors.affiliation: Innovative Drug Research Centre, Chongqing University, Chongqing, 401331, People's Republic of China. libibp@gmail.com.
authors.forename: Bo
authors.initials: B
authors.lastname: Li
authors.affiliation: Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, and Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Centre, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China. 412872021@qq.com.
authors.forename: Qi
authors.initials: Q
authors.lastname: Qi
authors.affiliation: Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, and Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Centre, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China. 404770794@qq.com.
authors.forename: Lei
authors.initials: L
authors.lastname: Wei
authors.affiliation: Wageningen University, Wageningen, 6708 PG, Netherlands. taiyi.zhao@wur.nl.
authors.forename: Taiyi
authors.initials: T
authors.lastname: Zhao
authors.affiliation: Guangzhou East Campus Lab Centre, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China. hejian22@mail.sysu.edu.cn.
authors.forename: Jian
authors.initials: J
authors.lastname: He
authors.affiliation: Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, and Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Centre, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China. cyfz@scau.edu.cn.
authors.forename: Jingchen
authors.initials: J
authors.lastname: Sun
mesh_terms: D000818:Animals; D012831:Bombyx / Q000235:genetics*; D003062:Codon / Q000235:genetics*; D017344:Genes, Insect / Q000235:genetics; D058977:Molecular Sequence Annotation; D009711:Nucleotides / Q000235:genetics; D014176:Protein Biosynthesis; D059467:Transcriptome
chemical_list: D003062:Codon; D009711:Nucleotides