Codon usage bias in the chloroplast genome of high production Coffea arabica L.

【Objective】This paper analyzed the codon usage pattern of chloroplast genome in high production Coffea arabica L. and the influencing factors of its codon usage bias, to determine the appropriate heterologous expression hostand provide reference basis for phylogenetic analysis and gene function verification of coffee, especially heterologous expression.【Method】The complete chloroplast genome sequence of high production C. arabica(MK353209) was retrieved and downloaded from the GenBank database. A total of 51 coding sequences(CDS) were selected, which had a length greater than 300 bp, started with ATG, ended with TAG, TAA and TGA, and had no stop codon or repetitive sequence. And this study systematically analyzed the characteristics of codon usage in the genome of high production C. arabica and its influencing factors, and compared the codon usage frequency with model organismsby using EMBOSS online website and CodonW 1.4.2 software.【Result】The results showed that the GC content of the first codon positions(GC1), second codon positions(GC2), third codon positions(GC3) and the average GC content of three positions(GC) in the genome of high production C. arabica were less than 50.00%. Among the 30 codons with RSCU>1.00, 96.67% codons ended with A/T and 3.33% codons ended with G/C, indicating that the chloroplast genome of high production C. arabica tended to end with A/T codons. The average values of effective number of codons(ENC), codon adaptation index(CAI), and optimal codon usage frequency(Fop) were 46.97, 0.167 and 0.353 respectively, indicated that the codon usage bias of chloroplast gene in high production C. arabica was weak. The 20 high-frequency codons were GCT, TGT, GAT, GAA, TTT, GGA, CAT, ATT, AAA, TTA, AAT, CCT, CAA, AGA, TCT, ACT, GTA, GTT, TAT and TAA. Neutral plot, ENC-plot, PR2-plot and correspondence analysis showed that codon usage bias was affected by natural selection, mutation and other factors, among which natural selection played adecisive role. The comparison of codon usage frequency found that there were 23.44%, 15.63%, 40.63% and 15.63% codon usage patterns of high production C.arabica varied considerably compared with those of Arabidopsis thaliana, Nicotiana tabacum, Escherichia coli and Saccharomyces cerevisiae respectively. Finally, 21 optimal codons were determined, among which 57.14% codons ended with T, 38.10% ended with A, and 4.76% ended with G.【Conclusion】The codon usage bias of the chloroplast genome of high production C. arabica is relatively weak, and tend to end with A/T codon. Codon usage bias is affected by many factors, such as natural selection, mutation, gene expression level, gene length and so on. S. cerevisiae and N. tabacum are more suitable for heterologous expression receptor systems of high production C. arabica genes.