Synonymous codon usage in chloroplast genome of Coffea arabica

Synonymous codon usage of 53 protein coding genes in chloroplast genome of Coffea arabica was analyzed for the first time to findout the possible factors contributing codon bias. All preferred synonymous codons were found to use A/T ending codons aschloroplast genomes are rich in AT. No difference in preference for preferred codons was observed in any of the two strands, viz.,leading and lagging strands. Complex correlations between total base compositions (A, T, G, C, GC) and silent base contents (A₃, T₃,G₃, C₃, GC₃) revealed that compositional constraints played crucial role in shaping the codon usage pattern of C. arabica chloroplastgenome. ENC Vs GC₃ plot grouped majority of the analyzed genes on or just below the left side of the expected GC₃ curveindicating the influence of base compositional constraints in regulating codon usage. But some of the genes lie distantly below thecontinuous curve confirmed the influence of some other factors on the codon usage across those genes. Influence of compositionalconstraints was further confirmed by correspondence analysis as axis 1 and 3 had significant correlations with silent base contents.Correlation of ENC with axis 1, 4 and CAI with 1, 2 prognosticated the minor influence of selection in nature but exact separationof highly and lowly expressed genes could not be seen. From the present study, we concluded that mutational pressure combinedwith weak selection influenced the pattern of synonymous codon usage across the genes in the chloroplast genomes of C. arabica.