Abstract:

Objective: Heterologous expression is an important means of plant protein function verification and molecular breeding. Codons are important factors for efficient expression of heterologous genes. An analysis of codon bias of gene coding region of Pinus massoniana transcriptome was conducted in order to provide a theoretical basis for molecular breeding of P. massoniana. Method: Analysis of codon parameters and bias in P. massoniana transcriptome by using CodonW, EMBOSS and other codon analysis software. According to the neutral mapping, ENc-GC3s correlation analysis and bias analysis speculates the main reasons for codon bias. The optimal codons of P. massoniana were screened by comparing the relative synonymous codon usage(RSCU) of high and low expression gene samples, and the codon bias differences between P. massoniana and Arabidopsis thaliana, Nicotiana tabacum, Populus tremula, Escherichia coli and Saccharomyces cerevisiae were analyzed by codon usage frequency ratio. Result: The average GC content of P. massoniana transcriptome coding sequence(CDS) codon was 44.95%, and GC content in the third position of codon was 38.95%, especially preferred A/T. Statistical analysis of high and low expression gene samples indicated that the difference of the relative synonymous codon usage (RSCU) in the transcriptome of P. massoniana was small, the 27 codons such as TTA, CAA, TGT and GGT can be used as the optimal codons for P. massoniana. Neutral mapping, ENc-GC3s correlation analysis and bias analysis showed that the formation of P. massoniana codon preference may be mainly affected by mutation, and secondly affected by multiple factors such as natural selection. Codon usage frequency analysis showed that the codon bias in P. massoniana was less different from N. tabacum, A. thaliana and P. tremula. The difference with E. coli was the largest, and the difference with S. cerevisiae was smaller than E. coli. Conclusion: Among the 27 optimal codons screened, 25 codons have the third one as A/T. P. massoniana prefers the third codon as A/T. The formation of P. massoniana codon preference may be mainly affected by mutation, and secondly affected by multiple factors such as natural selection. N. tabacum is the preferred plant organisms for heterologous expression of P. massoniana and S. cerevisiae may be superior to E. coli in the microorganism.

Key words: Pinus massoniana, transcriptome, codon usage bias